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- PDB-8c3v: SARS-CoV-2 Delta-RBD complexed with BA.2-13 Fab and C1 nanobody -

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Basic information

Entry
Database: PDB / ID: 8c3v
TitleSARS-CoV-2 Delta-RBD complexed with BA.2-13 Fab and C1 nanobody
Components
  • BA.2-13 heavy chainSARS-CoV-2 Omicron variant
  • BA.2-13 light chainSARS-CoV-2 Omicron variant
  • Nanobody C1
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / BA.2 mAb / RBD / BA.2-13 / BA.2-36 / VIRAL PROTEIN/Immune system
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Cell Rep / Year: 2023
Title: Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.
Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de ...Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de Silva / Megan Plowright / Thomas A H Newman / Hailey Hornsby / Alexander J Mentzer / Donal Skelly / Thomas G Ritter / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / / Cornelius Roemer / Thomas P Peacock / Neil G Paterson / Mark A Williams / David R Hall / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or ...In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (mAbs) generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum.
History
DepositionDec 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: BA.2-13 heavy chain
L: BA.2-13 light chain
R: Spike protein S1
I: Nanobody C1
X: Spike protein S1
J: Nanobody C1
Y: Spike protein S1
K: Nanobody C1
A: BA.2-13 heavy chain
B: BA.2-13 light chain
C: BA.2-13 heavy chain
D: BA.2-13 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,97433
Polymers256,53412
Non-polymers4,44021
Water0
1
H: BA.2-13 heavy chain
L: BA.2-13 light chain
R: Spike protein S1
I: Nanobody C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,98711
Polymers85,5114
Non-polymers1,4757
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Spike protein S1
J: Nanobody C1
A: BA.2-13 heavy chain
B: BA.2-13 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,01912
Polymers85,5114
Non-polymers1,5088
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
Y: Spike protein S1
K: Nanobody C1
C: BA.2-13 heavy chain
D: BA.2-13 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,96910
Polymers85,5114
Non-polymers1,4576
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.925, 160.817, 172.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(heavy chain / chain "A" / chain "I" and (resid...
d_2ens_1(heavy chain / chain "C" and (resid 1 through 29 or resid 31 through 227))
d_1ens_2(light chain / chain "B" / chain "J" and (resid 1 through 79 or resid 82 through 212))
d_2ens_2(light chain / chain "D" / chain "L" (resid 1 through 79 or resid 82 through 212))
d_1ens_3(nanobody / chain "I" / chain "D" and resid 1 through 124)
d_2ens_3(nanobody / chain "J" / chain "F" and resid 1 through 124)
d_3ens_3(nanobody / chain "K" / chain "H" and resid 1 through 124)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLNGLNPHEPHEAI1 - 291 - 29
d_12ens_1TYRTYRSERSERAI31 - 14031 - 140
d_13ens_1GLYGLYLYSLYSAI147 - 227147 - 227
d_21ens_1GLNGLNPHEPHECK1 - 291 - 29
d_22ens_1TYRTYRLYSLYSCK31 - 22731 - 227
d_11ens_2ASPASPGLNGLNBJ1 - 791 - 79
d_12ens_2ASPASPGLUGLUBJ82 - 21282 - 212
d_21ens_2ASPASPGLNGLNDL1 - 791 - 79
d_22ens_2ASPASPGLUGLUDL82 - 21282 - 212
d_11ens_3GLNGLNSERSERID1 - 1241 - 124
d_21ens_3GLNGLNSERSERJF1 - 1241 - 124
d_31ens_3GLNGLNSERSERKH1 - 1241 - 124

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.390088657649, -0.895043185911, -0.216167838791), (0.917623294886, -0.397302321476, -0.0108790639632), (-0.0761467521106, -0.202604443937, 0.976295606586)85.1058415948, 41.8268933262, 13.0627754488
2given(-0.387362626111, -0.908699747692, -0.155611581949), (0.920174930449, -0.391481455569, -0.00451301651068), (-0.0568180716401, -0.144938050524, 0.987808011835)80.5800417858, 40.815606715, 11.2345189673
3given(-0.485415639762, -0.844666718946, -0.225631980403), (0.869036955581, -0.494388362632, -0.0188392337531), (-0.095636951587, -0.205227388036, 0.974030437251)87.6891720765, 46.3439099929, 13.0035244689
4given(-0.469219620972, 0.880931817076, -0.0615798746203), (-0.842310455544, -0.467410575805, -0.268403521041), (-0.265228286154, -0.0740708261664, 0.961336293362)1.36758717374, 99.9777946114, 12.5214265232

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Components

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Protein , 1 types, 3 molecules RXY

#3: Protein Spike protein S1


Mass: 22935.734 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

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Antibody , 3 types, 9 molecules HACLBDIJK

#1: Antibody BA.2-13 heavy chain / SARS-CoV-2 Omicron variant


Mass: 24766.760 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody BA.2-13 light chain / SARS-CoV-2 Omicron variant


Mass: 23149.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Nanobody C1


Mass: 14659.114 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Sugars , 3 types, 3 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 18 molecules

#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BICINE pH 8.5, 15% PEG 1,500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.74→80 Å / Num. obs: 78088 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 75.46 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.072 / Net I/σ(I): 7.4
Reflection shellResolution: 2.74→2.79 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 3830 / CC1/2: 0.317

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Processing

Software
NameVersionClassification
GDA1.20.1_4487data collection
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BBO

8bbo


Resolution: 2.74→66.87 Å / SU ML: 0.4679 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 3933 5.05 %
Rwork0.2156 73941 -
obs0.2177 77874 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.88 Å2
Refinement stepCycle: LAST / Resolution: 2.74→66.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17512 0 295 0 17807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003418221
X-RAY DIFFRACTIONf_angle_d0.611424727
X-RAY DIFFRACTIONf_chiral_restr0.0442730
X-RAY DIFFRACTIONf_plane_restr0.00453161
X-RAY DIFFRACTIONf_dihedral_angle_d12.57256531
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.28114405596
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.33216564881
ens_3d_2IX-RAY DIFFRACTIONTorsion NCS0.180100151335
ens_3d_3JX-RAY DIFFRACTIONTorsion NCS0.179976287088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.770.37531360.38252576X-RAY DIFFRACTION98.15
2.77-2.810.37941420.36672581X-RAY DIFFRACTION99.63
2.81-2.850.36861300.36042596X-RAY DIFFRACTION99.71
2.85-2.880.38351330.34822616X-RAY DIFFRACTION99.64
2.88-2.930.34691300.34682626X-RAY DIFFRACTION99.75
2.93-2.970.35861530.32412614X-RAY DIFFRACTION99.89
2.97-3.020.33891360.31952600X-RAY DIFFRACTION99.78
3.02-3.060.3281530.3112593X-RAY DIFFRACTION99.89
3.06-3.120.32981320.31522638X-RAY DIFFRACTION99.96
3.12-3.170.36641380.29892591X-RAY DIFFRACTION99.96
3.17-3.240.35421560.29542609X-RAY DIFFRACTION99.93
3.24-3.30.30251240.26642639X-RAY DIFFRACTION99.89
3.3-3.370.29021360.26742638X-RAY DIFFRACTION99.82
3.37-3.450.30571410.25732623X-RAY DIFFRACTION99.89
3.45-3.540.30841510.25152622X-RAY DIFFRACTION100
3.54-3.630.25191330.23262646X-RAY DIFFRACTION100
3.63-3.740.27031530.23012614X-RAY DIFFRACTION99.96
3.74-3.860.26871380.23342627X-RAY DIFFRACTION99.93
3.86-40.31491470.22552637X-RAY DIFFRACTION99.93
4-4.160.22681290.19282656X-RAY DIFFRACTION100
4.16-4.350.22661430.17172657X-RAY DIFFRACTION100
4.35-4.580.20191630.15892642X-RAY DIFFRACTION100
4.58-4.860.18931280.15872656X-RAY DIFFRACTION99.96
4.87-5.240.19091330.16392688X-RAY DIFFRACTION100
5.24-5.770.22611430.17442689X-RAY DIFFRACTION100
5.77-6.60.23061250.19052721X-RAY DIFFRACTION100
6.6-8.310.25331410.19942729X-RAY DIFFRACTION100
8.32-66.870.21681660.1672817X-RAY DIFFRACTION98.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.782278733811.47116898717-1.284353310432.87665643939-2.578878995752.505719854070.316076321038-0.472347409213-0.518696503680.585807056347-0.004593153944540.3395634246140.1765393510830.0203128012636-0.06298845709060.831534331654-0.244124314007-0.03964110239790.8082058361890.1868601192290.92635170101843.789526311234.854803477674.2489450831
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33.069154401151.13686854612-1.292559805385.08682191333-1.255591004670.8537412086890.08364904104370.2143933654110.6029785117581.17941416098-0.105525952972-0.135592903087-0.3247812304751.049545889520.1007132588710.295842085141-0.0645678117392-0.101125197540.748084624393-0.03089773025871.0079607453262.549192205150.216546128457.3301648716
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493.90921577355-1.42333634680.8433044264081.90963671732-0.01220946955911.110810057930.266659370494-0.1696959550831.2296995885-0.5135460598760.1159176860160.165459722915-0.0114759210193-0.1904795958770.01099487723670.766312070298-0.0947266084527-0.08502965081130.6956620104260.2871635751651.6106529026117.576250744891.353124786427.4014122567
501.920242497660.0876524520030.1708331960931.1719551591-0.3736947266221.19215924153-0.2353340955070.4395341308091.036996287140.0726742581752-0.192427856878-0.0284940134225-0.0264174707641-0.0967691354541-0.0190207803310.665392257204-0.03961857499690.01099685508850.562565298250.1925434383191.2852017582421.31831729380.030353417232.7790238808
510.7492344870980.9477467420250.09551110536181.43961368484-0.02065835818613.28851163461-0.1762193240510.01682411174680.2567328340590.733574850291-0.1541153235120.257893085755-0.0652713577292-0.497269618175-0.05676029695950.770446986541-0.03115132216070.07154326208560.672850896139-0.009551826691171.497790185939.6297075860684.118275674636.2182762592
523.19128532467-1.433176623460.1308935851933.427274519660.1121866276962.554277916150.1893359915340.5859241150770.747102172665-0.8029679467550.1778286289410.405504198132-0.19609720558-0.24500585709-0.0123500969210.54627289311-0.0349660100618-0.06748610334970.6805243006980.09572096930271.0278709695412.403689341178.318669518824.7550735346
533.514745484321.57256851928-0.312894943480.74236579987-0.5098239338012.149338944750.384634689802-0.03898725411580.398360598676-1.14349143728-0.01051689205930.0998359965748-0.395303017797-0.03058701178110.003999181578080.867409767713-0.00054536414778-0.04256681391090.6744731667740.3692603194251.4969462936420.74416914284.828321360322.7126947272
540.784974138355-0.4722222031560.427059207690.406952822013-0.3709035437231.541133609530.4662895341560.3926023676121.01323827313-0.575100928092-0.697082393775-0.5347020841490.0108800913638-0.3896650245160.001350783425670.7750675895450.00423525560574-0.1177716824680.8681164883310.2826047253191.691322030638.4033704570489.385881874530.088412657
551.367857317960.1219733844020.04482734710361.08749963631-0.2439795494161.80692444236-0.2563056321210.06132522874760.8628743140230.3046546322580.0344565007339-0.04003792250360.00581069485554-0.02016501029440.008248660709240.563761196602-0.0447599492766-0.0129041535310.5914935649340.03208765105711.241471398718.380984836179.392645411938.9921850858
562.939188058990.16740939088-1.101666921390.4467492553870.2853130626770.688079684650.6529935765990.478364095853-0.2336381023050.3353828576430.6472313969980.464238631910.13710115592-0.3854972581330.3623563779540.2458459494460.299092309182-0.1626640134570.9017129528650.1961181666872.736546953927.0496373834197.560280180629.1910239323
570.853509570314-0.257519697563-0.4696805978310.429858759231-0.04076833894830.354215017591-0.232548533639-0.105641444980.0901980111733-0.2298885627960.12398390085-0.0237613397750.1940882835310.211376199539-0.128858213530.5245328036290.02034856281170.006831856992010.589349935402-0.08157589112090.74855752301632.413820886326.127148885638.7273181065
581.161534671580.161191495955-1.438864241550.302614393898-0.5362261269431.88153887707-0.41495873397-0.09130141517620.279942390277-0.01450001127530.148672876515-0.1081100744920.791018732670.04458094814210.01037471573070.576456471663-0.0182108515530.04473607872970.642394023126-0.0001739283678130.73180498784226.007822651731.21928477442.6463124318
591.210615181720.4758950040240.03482914386941.098309502430.06927637442952.19340609816-0.1776490199280.0017305605820.121611428833-0.2582370654280.09300693012140.04207009154590.2189643347890.0952799796722-0.0337233778550.4720993350910.00104614882038-0.006127550805690.517590758465-0.02592921390690.75989005788317.534662505227.741378424935.0777750114
602.9446578848-0.9500721203631.178139717632.048159562041.722743299183.03037757329-0.2202400299880.5230680014180.4644706298750.1598999013670.07450408321721.456245123930.414918708852-0.169628977322-0.03918226901060.5232732082860.05648846715160.09029974446020.6521787774530.05467002954230.6093615327726.6539185968728.250332428548.4616334503
610.902596018280.308459130451-0.448089749250.869207312854-0.5697433988731.960470840470.00883029468402-0.1377510627110.0344122388223-0.2241868227960.1318674182590.1557824046160.16179574466-0.179334520273-0.01375720856960.481178710593-0.013823515967-0.03239329792880.489976078796-0.00660361451380.66832318223215.191775112722.149268768448.8838706499
621.189260096150.5747581587050.362559467010.72470617289-0.6489889167852.769060767520.133413683242-0.4850498829920.6096191318820.1542032252760.124979444818-0.624617873999-0.747149388444-0.2373188002570.004612500691180.592979301917-0.0642137251911-0.05892819186980.5152011957810.003866259121620.85495007354914.355619602134.151882927853.9190825277
632.92219346545-2.55774638124-3.593261641762.961213456342.941843350936.398476966860.2925359528050.8312398878980.4678582089580.8355116924150.3456849404620.458461238415-0.07297925969710.135323042675-0.2200056867010.8121709150510.1714776681220.1299562095010.9265264097770.03561593878970.6983043643827.2872449977828.994296386570.5715261443
642.520450064750.678600397598-0.7342962383270.608670738851-1.009239813872.28021375293-0.414300902011-0.782536632909-0.7697621578780.158096475951-0.7256635154930.7277456781070.0461116892649-0.2793385615330.04085887270230.747033421820.04724537321530.07947954224930.7519998159880.0445411693450.9353900112339.5816260301722.974594072569.3135682557
650.879084820491.037174217171.098948795711.426664384720.9933892104712.20785855371-0.0857710713015-0.452785202920.1256534952340.06162117072640.6274862486970.06540891604471.13283982569-0.289802362739-0.009760341956740.798576122917-0.02357435601720.01206603584820.6453091494320.05043763882160.77214585362512.49917258739.6562324970248.8843603095
660.4485436719180.258684444458-0.3706735851314.3832983935-1.575976703631.444462665330.243958324150.187406458313-0.135778523798-0.3238205386140.2140313766760.9708687226440.0305035589291-0.0320046871464-0.02522273592270.440997294859-0.0684084490205-0.04779239474430.552633477663-0.01797413804340.65305025773520.139342488535.5422240934.6054545338
670.9841507676260.6984901389390.9731389001092.89306912744-0.08171300061841.14836223870.0172195519530.9865544732760.639401291427-0.987261663083-0.5864112386611.225589046240.6487460107760.02409960825110.007004341210971.25069896883-0.0351453909531-0.3107399188581.00012464320.02147438962050.971573268812-4.9691492461614.270075389419.8126112906
681.95068011130.198798738915-0.2591023172512.26695955229-0.2340603973511.12800978489-0.2209293095440.06808131947250.414622951443-0.767703509842-0.2609159624970.7958467866680.159310020922-0.143771448383-0.07668246122370.882700160979-0.09546895296-0.2306262320970.5784046747950.1232212854020.8385338117060.57838850141420.171286557125.5506283823
692.764862782970.250283791037-1.190845427881.398842954920.06202380458882.689580382960.4385175339040.516540730104-0.0226411186424-0.428074747273-0.7270840004120.2861099793580.5988088585630.6759943374550.001000986237550.8700349557160.04485313221850.0224969261690.6695021505240.1869551444030.7041183859768.7828064939120.181274644324.7669498157
700.9464532893551.05785255816-0.614183927041.811453748930.006972161948791.08884915873-0.6921032407721.50246857513-0.23217174397-0.934059289306-0.0625421333604-0.4258684383310.7263285119030.64769100506-0.03626096658711.67269623223-0.006225265030290.08878782056820.7208354220250.09634745767880.7064443223648.9905751113114.420620692518.8499197194
713.684653750410.4804937627690.1900834430040.14396012481-0.4984538850044.20586843581-0.1809266818550.1599857822281.21908552624-0.62833248186-0.01117450193090.1308093551841.49167353647-0.337775203877-0.01619750934951.47585776646-0.161889133779-0.2452606411910.7809849955440.0902571844970.9053057365140.7574631338521.96315219415.7515971677
724.29819167752-1.90613473891-1.663514153241.612486200451.442322064671.27852251377-0.0009147197059330.280173963357-1.05646612776-1.15124567690.21026332146-0.1750183009960.337042889984-0.1266968445710.01163504296342.53373503297-0.161084482606-0.08313785639570.8241478406-0.05901229614270.9350696371014.064286005413.0685244646819.4831439474
732.201952074180.3931857512560.1753550281860.987183459279-1.099771754591.722768389730.382295656786-0.3222387266280.279360831702-0.490791696296-0.01060525716410.7285435920190.308807347078-0.330755027387-0.03470397365460.664219622835-0.0616899496311-0.1411521391130.5761644530130.02778643819690.8845700786052.3752080437420.684570793731.6337323318
742.273381991792.115747449911.120981451772.694863195380.4183506731881.57430184698-0.0748295715169-0.2498335910020.139070396958-0.650280514408-0.04234626125830.4704822011111.57166563139-0.04362053350350.02205152390491.50744278508-0.154501194999-0.4389107204070.752921591987-0.04640731883671.08824257897-5.707610120996.2912731010822.2153401728
750.4164164419550.1174550218340.02298690005490.738899334655-0.7963232179230.513319098376-0.1034310256340.2619386418020.306198210560.08686114714480.02568010005760.161331034184-0.02679181402110.163379591893-0.2118454683660.522290058577-0.05293187890730.01472274870020.652116853660.08003481418110.87488950035541.176045251760.177710732942.6487705474
760.598099482057-0.2767604522880.2749289138470.533428443149-1.067010102091.699001765760.135979126581-0.0710081802884-0.113961550401-0.07142971730610.0274156987576-0.161105284918-0.3039985974740.1773346238920.04556824623210.501039953915-0.05283780329250.005953377122730.5551364498560.006343792579520.79079316500144.348540148752.064464569941.3907654646
771.988731083470.4081363252350.6287438474741.3551157940.4305561728551.529774192420.1042868460710.0314368128759-0.4618502638840.1295817948720.140399074068-0.2264680869770.1791721834080.1187733353480.03669097948220.4680627074840.01014074325910.0315469328590.5128748868360.01104919118910.81815133610247.310000842942.859120105943.8410183191
780.840528653074-0.2794130539710.5032714278710.2223164156610.3529206991682.56874202144-0.04040506762020.0755905622507-0.2199402950310.09514581308470.135983694392-0.1393329102620.1589291945290.1402575327460.0536868029050.428339658273-0.018355488622-0.02658377983720.5067214816670.00405456444510.73516687711148.356525600545.021905925854.8556367213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'Y' and (resid 470 through 479 )Y470 - 479
2X-RAY DIFFRACTION2chain 'Y' and (resid 480 through 494 )Y480 - 494
3X-RAY DIFFRACTION3chain 'Y' and (resid 495 through 506 )Y495 - 506
4X-RAY DIFFRACTION4chain 'Y' and (resid 507 through 525 )Y507 - 525
5X-RAY DIFFRACTION5chain 'K' and (resid 1 through 25 )K1 - 25
6X-RAY DIFFRACTION6chain 'K' and (resid 26 through 60 )K26 - 60
7X-RAY DIFFRACTION7chain 'K' and (resid 61 through 73 )K61 - 73
8X-RAY DIFFRACTION8chain 'K' and (resid 74 through 124 )K74 - 124
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 158 )A1 - 158
10X-RAY DIFFRACTION10chain 'A' and (resid 159 through 170 )A159 - 170
11X-RAY DIFFRACTION11chain 'A' and (resid 171 through 228 )A171 - 228
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 101 )B1 - 101
13X-RAY DIFFRACTION13chain 'B' and (resid 102 through 127 )B102 - 127
14X-RAY DIFFRACTION14chain 'B' and (resid 128 through 173 )B128 - 173
15X-RAY DIFFRACTION15chain 'B' and (resid 174 through 212 )B174 - 212
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 17 )C1 - 17
17X-RAY DIFFRACTION17chain 'C' and (resid 18 through 44 )C18 - 44
18X-RAY DIFFRACTION18chain 'C' and (resid 45 through 93 )C45 - 93
19X-RAY DIFFRACTION19chain 'C' and (resid 94 through 116 )C94 - 116
20X-RAY DIFFRACTION20chain 'C' and (resid 117 through 132 )C117 - 132
21X-RAY DIFFRACTION21chain 'C' and (resid 133 through 158 )C133 - 158
22X-RAY DIFFRACTION22chain 'C' and (resid 159 through 201 )C159 - 201
23X-RAY DIFFRACTION23chain 'C' and (resid 202 through 216 )C202 - 216
24X-RAY DIFFRACTION24chain 'C' and (resid 217 through 227 )C217 - 227
25X-RAY DIFFRACTION25chain 'D' and (resid 1 through 18 )D1 - 18
26X-RAY DIFFRACTION26chain 'D' and (resid 19 through 75 )D19 - 75
27X-RAY DIFFRACTION27chain 'D' and (resid 76 through 101 )D76 - 101
28X-RAY DIFFRACTION28chain 'D' and (resid 102 through 112 )D102 - 112
29X-RAY DIFFRACTION29chain 'D' and (resid 113 through 143 )D113 - 143
30X-RAY DIFFRACTION30chain 'D' and (resid 144 through 154 )D144 - 154
31X-RAY DIFFRACTION31chain 'D' and (resid 155 through 173 )D155 - 173
32X-RAY DIFFRACTION32chain 'D' and (resid 174 through 196 )D174 - 196
33X-RAY DIFFRACTION33chain 'D' and (resid 197 through 212 )D197 - 212
34X-RAY DIFFRACTION34chain 'H' and (resid 1 through 17 )H1 - 17
35X-RAY DIFFRACTION35chain 'H' and (resid 18 through 44 )H18 - 44
36X-RAY DIFFRACTION36chain 'H' and (resid 45 through 132 )H45 - 132
37X-RAY DIFFRACTION37chain 'H' and (resid 133 through 158 )H133 - 158
38X-RAY DIFFRACTION38chain 'H' and (resid 159 through 201 )H159 - 201
39X-RAY DIFFRACTION39chain 'H' and (resid 202 through 227 )H202 - 227
40X-RAY DIFFRACTION40chain 'L' and (resid 1 through 25 )L1 - 25
41X-RAY DIFFRACTION41chain 'L' and (resid 26 through 100 )L26 - 100
42X-RAY DIFFRACTION42chain 'L' and (resid 101 through 112 )L101 - 112
43X-RAY DIFFRACTION43chain 'L' and (resid 113 through 127 )L113 - 127
44X-RAY DIFFRACTION44chain 'L' and (resid 128 through 212 )L128 - 212
45X-RAY DIFFRACTION45chain 'R' and (resid 329 through 349 )R329 - 349
46X-RAY DIFFRACTION46chain 'R' and (resid 350 through 479 )R350 - 479
47X-RAY DIFFRACTION47chain 'R' and (resid 480 through 494 )R480 - 494
48X-RAY DIFFRACTION48chain 'R' and (resid 495 through 525 )R495 - 525
49X-RAY DIFFRACTION49chain 'I' and (resid 1 through 25 )I1 - 25
50X-RAY DIFFRACTION50chain 'I' and (resid 26 through 39 )I26 - 39
51X-RAY DIFFRACTION51chain 'I' and (resid 40 through 52 )I40 - 52
52X-RAY DIFFRACTION52chain 'I' and (resid 53 through 73 )I53 - 73
53X-RAY DIFFRACTION53chain 'I' and (resid 74 through 83 )I74 - 83
54X-RAY DIFFRACTION54chain 'I' and (resid 84 through 99 )I84 - 99
55X-RAY DIFFRACTION55chain 'I' and (resid 100 through 117 )I100 - 117
56X-RAY DIFFRACTION56chain 'I' and (resid 118 through 124 )I118 - 124
57X-RAY DIFFRACTION57chain 'X' and (resid 329 through 349 )X329 - 349
58X-RAY DIFFRACTION58chain 'X' and (resid 350 through 364 )X350 - 364
59X-RAY DIFFRACTION59chain 'X' and (resid 365 through 409 )X365 - 409
60X-RAY DIFFRACTION60chain 'X' and (resid 410 through 421 )X410 - 421
61X-RAY DIFFRACTION61chain 'X' and (resid 422 through 459 )X422 - 459
62X-RAY DIFFRACTION62chain 'X' and (resid 460 through 469 )X460 - 469
63X-RAY DIFFRACTION63chain 'X' and (resid 470 through 479 )X470 - 479
64X-RAY DIFFRACTION64chain 'X' and (resid 480 through 494 )X480 - 494
65X-RAY DIFFRACTION65chain 'X' and (resid 495 through 506 )X495 - 506
66X-RAY DIFFRACTION66chain 'X' and (resid 507 through 525 )X507 - 525
67X-RAY DIFFRACTION67chain 'J' and (resid 1 through 17 )J1 - 17
68X-RAY DIFFRACTION68chain 'J' and (resid 18 through 44 )J18 - 44
69X-RAY DIFFRACTION69chain 'J' and (resid 45 through 60 )J45 - 60
70X-RAY DIFFRACTION70chain 'J' and (resid 61 through 73 )J61 - 73
71X-RAY DIFFRACTION71chain 'J' and (resid 74 through 83 )J74 - 83
72X-RAY DIFFRACTION72chain 'J' and (resid 84 through 91 )J84 - 91
73X-RAY DIFFRACTION73chain 'J' and (resid 92 through 115 )J92 - 115
74X-RAY DIFFRACTION74chain 'J' and (resid 116 through 124 )J116 - 124
75X-RAY DIFFRACTION75chain 'Y' and (resid 329 through 349 )Y329 - 349
76X-RAY DIFFRACTION76chain 'Y' and (resid 350 through 375 )Y350 - 375
77X-RAY DIFFRACTION77chain 'Y' and (resid 376 through 421 )Y376 - 421
78X-RAY DIFFRACTION78chain 'Y' and (resid 422 through 469 )Y422 - 469

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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