[English] 日本語
Yorodumi
- PDB-4pos: Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pos
TitleStructure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactosamine
ComponentsVP1
KeywordsVIRAL PROTEIN / jelly roll fold / capsid formation / receptor interaction / carbohydrate / sialyloligosaccharide / viral coat protein
Function / homology
Function and homology information


T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus Vp1; Chain A / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
3'-sialyl-N-acetyllactosamine / ISOPROPYL ALCOHOL / Capsid protein VP1
Similarity search - Component
Biological speciesHuman polyomavirus 9
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKhan, Z.M. / Stehle, T.
CitationJournal: J.Virol. / Year: 2014
Title: Crystallographic and glycan microarray analysis of human polyomavirus 9 VP1 identifies N-glycolyl neuraminic acid as a receptor candidate.
Authors: Khan, Z.M. / Liu, Y. / Neu, U. / Gilbert, M. / Ehlers, B. / Feizi, T. / Stehle, T.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_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_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,51569
Polymers301,58010
Non-polymers8,93559
Water45,4522523
1
A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,92034
Polymers150,7905
Non-polymers4,13029
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31310 Å2
ΔGint-121 kcal/mol
Surface area47920 Å2
MethodPISA
2
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,59535
Polymers150,7905
Non-polymers4,80530
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32900 Å2
ΔGint-118 kcal/mol
Surface area48140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.910, 180.630, 199.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEUAA46 - 5220 - 26
21THRTHRLEULEUBB46 - 5220 - 26
31THRTHRLEULEUCC46 - 5220 - 26
41THRTHRLEULEUDD46 - 5220 - 26
51THRTHRLEULEUEE46 - 5220 - 26
61THRTHRLEULEUFF46 - 5220 - 26
71THRTHRLEULEUGG46 - 5220 - 26
81THRTHRLEULEUHH46 - 5220 - 26
91THRTHRLEULEUII46 - 5220 - 26
101THRTHRLEULEUJJ46 - 5220 - 26
12GLYGLYGLYGLYAA140 - 160114 - 134
22GLYGLYGLYGLYBB140 - 160114 - 134
32GLYGLYGLYGLYCC140 - 160114 - 134
42GLYGLYGLYGLYDD140 - 160114 - 134
52GLYGLYGLYGLYEE140 - 160114 - 134
62GLYGLYGLYGLYFF140 - 160114 - 134
72GLYGLYGLYGLYGG140 - 160114 - 134
82GLYGLYGLYGLYHH140 - 160114 - 134
92GLYGLYGLYGLYII140 - 160114 - 134
102GLYGLYGLYGLYJJ140 - 160114 - 134
13ASPASPVALVALAA250 - 268224 - 242
23ASPASPVALVALBB250 - 268224 - 242
33ASPASPVALVALCC250 - 268224 - 242
43ASPASPVALVALDD250 - 268224 - 242
53ASPASPVALVALEE250 - 268224 - 242
63ASPASPVALVALFF250 - 268224 - 242
73ASPASPVALVALGG250 - 268224 - 242
83ASPASPVALVALHH250 - 268224 - 242
93ASPASPVALVALII250 - 268224 - 242
103ASPASPVALVALJJ250 - 268224 - 242
14SERSERPROPROAA280 - 287254 - 261
24SERSERPROPROBB280 - 287254 - 261
34SERSERPROPROCC280 - 287254 - 261
44SERSERPROPRODD280 - 287254 - 261
54SERSERPROPROEE280 - 287254 - 261
64SERSERPROPROFF280 - 287254 - 261
74SERSERPROPROGG280 - 287254 - 261
84SERSERPROPROHH280 - 287254 - 261
94SERSERPROPROII280 - 287254 - 261
104SERSERPROPROJJ280 - 287254 - 261

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.311726, 0.747854, -0.586124), (-0.683344, 0.605061, 0.408585), (0.660203, 0.273158, 0.699655)18.60553, 19.42274, -18.44719
3given(-0.802332, 0.519845, -0.293299), (-0.35834, -0.026539, 0.933214), (0.477343, 0.853848, 0.207574)49.13464, 11.22408, -14.03958
4given(-0.79968, -0.361954, 0.479062), (0.519366, -0.016635, 0.85439), (-0.301281, 0.932047, 0.201289)49.93406, -12.47107, 6.81693
5given(0.317284, -0.67609, 0.665006), (0.739265, 0.615552, 0.273098), (-0.593984, 0.404966, 0.695115)20.2246, -19.58803, 15.71243
6given(-0.855093, -0.402815, 0.32643), (-0.388692, 0.08138, -0.917767), (0.343125, -0.911656, -0.226159)45.61149, -43.31053, -70.83093
7given(-0.766137, 0.466371, -0.44219), (0.477921, -0.046578, -0.877167), (-0.429682, -0.883362, -0.187204)42.10028, -66.77619, -49.82066
8given(0.360679, 0.639884, -0.678571), (0.642792, -0.697706, -0.316267), (-0.675817, -0.32211, -0.66296)11.29791, -70.51871, -43.86893
9given(0.988844, -0.14019, -0.050344), (-0.140263, -0.990112, 0.002091), (-0.050139, 0.004994, -0.99873)-4.76908, -48.71139, -61.40253
10given(0.237558, -0.781265, 0.577227), (-0.777966, -0.508857, -0.368556), (0.581666, -0.361509, -0.728681)16.58204, -32.15887, -78.03145

-
Components

-
Protein / Sugars , 2 types, 19 molecules ABCDEFGHIJ

#1: Protein
VP1 / Major Capsid Protein


Mass: 30157.977 Da / Num. of mol.: 10 / Fragment: UNP residues 32-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human polyomavirus 9 / Gene: gp3, vp1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E9NQ90
#2: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 2573 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2523 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.15
Details: 20% v/v isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 5.15, soaked in 40 mM 3'-sialyllactosamine for 20 minutes, cryoprotectant: 25% v/v ethylene glycol, VAPOR DIFFUSION, ...Details: 20% v/v isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 5.15, soaked in 40 mM 3'-sialyllactosamine for 20 minutes, cryoprotectant: 25% v/v ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 30, 2012 / Details: mirrors
RadiationMonochromator: Bartels Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→133.876 Å / Num. all: 230735 / Num. obs: 235564 / % possible obs: 97.95 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 28.26 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.97
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.81 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.95 / Num. unique all: 16974 / % possible all: 98.02

-
Processing

Software
NameVersionClassification
RemDAqdata collection
MOLREPphasing
REFMAC5.8.0025refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4POQ

4poq


Resolution: 2→133.876 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.128 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21318 11549 5 %RANDOM
Rwork0.17856 ---
all0.1803 230735 --
obs0.1803 219186 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.179 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å2-0 Å2-0 Å2
2---0.49 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2→133.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20646 0 584 2523 23753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221746
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.99829673
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17752721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75625.583849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.703153456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1651571
X-RAY DIFFRACTIONr_chiral_restr0.0760.23511
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02116127
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.651.39710878
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1472.35113595
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.071.63410868
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.9546.25736254
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A216MEDIUM POSITIONAL0.080.5
2B216MEDIUM POSITIONAL0.090.5
3C216MEDIUM POSITIONAL0.090.5
4D216MEDIUM POSITIONAL0.080.5
5E216MEDIUM POSITIONAL0.090.5
6F216MEDIUM POSITIONAL0.10.5
7G216MEDIUM POSITIONAL0.10.5
8H216MEDIUM POSITIONAL0.150.5
9I216MEDIUM POSITIONAL0.060.5
10J216MEDIUM POSITIONAL0.110.5
1A175LOOSE POSITIONAL0.165
2B175LOOSE POSITIONAL0.185
3C175LOOSE POSITIONAL0.175
4D175LOOSE POSITIONAL0.225
5E175LOOSE POSITIONAL0.225
6F175LOOSE POSITIONAL0.195
7G175LOOSE POSITIONAL0.235
8H175LOOSE POSITIONAL0.465
9I175LOOSE POSITIONAL0.165
10J175LOOSE POSITIONAL0.245
1A216MEDIUM THERMAL0.82
2B216MEDIUM THERMAL0.912
3C216MEDIUM THERMAL0.692
4D216MEDIUM THERMAL0.942
5E216MEDIUM THERMAL0.792
6F216MEDIUM THERMAL1.12
7G216MEDIUM THERMAL0.982
8H216MEDIUM THERMAL0.952
9I216MEDIUM THERMAL0.672
10J216MEDIUM THERMAL1.082
1A175LOOSE THERMAL1.0510
2B175LOOSE THERMAL1.3510
3C175LOOSE THERMAL1.1510
4D175LOOSE THERMAL1.6510
5E175LOOSE THERMAL1.1210
6F175LOOSE THERMAL1.3610
7G175LOOSE THERMAL1.3110
8H175LOOSE THERMAL1.0910
9I175LOOSE THERMAL0.9810
10J175LOOSE THERMAL1.5310
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 895 -
Rwork0.285 16039 -
obs-16039 97.9 %
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)
10.7161-0.00030.31552.7843.75798.2216-0.0286-0.00130.152-0.33070.0574-0.0826-0.63080.3431-0.02890.2085-0.01120.01920.10780.010.08252.2392-39.6427-57.0261
20.3962-0.15260.00272.39921.00562.0534-0.02090.01120.0542-0.00370.1755-0.3071-0.13510.3601-0.15450.21210.03050.0250.11-0.01490.046652.8155-47.9544-55.6965
30.3420.00810.14230.75780.02480.62150.00110.01810.0062-0.01090.0052-0.090.04140.0822-0.00630.25110.03520.01740.0763-0.00330.012343.5525-55.3005-59.9563
41.13460.85471.16222.1782.31623.43260.0218-0.0529-0.02380.01990.0688-0.1222-0.0320.088-0.09060.23990.03670.020.05030.00920.014247.0171-44.5806-55.1659
51.4721.59472.75663.7515.16558.7866-0.1413-0.0670.2613-0.1008-0.26590.3349-0.2993-0.27320.40720.33890.0056-0.0010.07010.00950.085725.6795-20.6324-70.191
60.58940.25070.20111.70381.37161.8969-0.0546-0.01080.0955-0.29150.0802-0.0855-0.2440.1764-0.02560.35180.0075-0.00860.09150.02680.042631.7966-25.5866-73.9309
70.6865-0.02570.09390.38660.1520.50650.0020.05690.0572-0.11110.0019-0.0264-0.02360.0441-0.00390.31990.01670.00270.05910.01640.009431.3756-37.7392-73.9006
80.57770.75710.57743.7642.40142.469-0.0109-0.01510.0445-0.10730.0131-0.0139-0.07960.124-0.00210.24990.02160.0040.05760.01270.011128.3773-27.578-68.9438
92.07533.41622.158410.63286.35814.29330.1227-0.25590.25050.6025-0.40740.61630.1847-0.43940.28470.29790.0437-0.02590.1989-0.01880.1254-2.457-24.8244-48.1708
100.90150.2433-0.17730.77390.33891.4911-0.01010.03780.0235-0.1518-0.11230.2991-0.0471-0.36780.12250.31260.0187-0.06450.1492-0.02710.1263-3.044-41.2174-72.8853
1140.5507-8.014120.93516.538411.047826.4795-1.00080.03830.59860.4568-0.68931.6362-0.2505-0.9031.69020.69930.1147-0.04920.5630.15910.8849-8.1601-6.9999-51.0584
120.421-0.0116-0.15050.5367-0.05070.82770.0185-0.00030.0395-0.0685-0.05950.1156-0.0645-0.1060.0410.25870.0028-0.03060.0973-0.00370.04014.6875-37.6907-65.5519
132.4969-0.8667-1.257810.74514.25088.296-0.2495-0.4154-0.05010.86710.3483-0.12160.27960.0712-0.09880.317-0.07880.08540.1954-0.02390.05432.2075-44.5359-23.129
140.8171-0.1239-0.20161.07880.92011.7494-0.0143-0.0392-0.07460.1066-0.05950.1960.1419-0.16480.07380.3139-0.06760.02350.10940.00510.0977-1.7666-64.6352-44.8119
150.4291-0.1591-0.07970.46490.18820.7280.0033-0.0048-0.0050.0251-0.02250.09530.0559-0.1240.01920.2611-0.04040.01180.1033-0.00770.0513.8941-58.1222-48.5593
1641.052630.2253-21.110422.347-15.779111.5414-0.2971.3686-0.5194-0.08211.0217-0.0172-0.2129-1.1104-0.72460.4560.2240.38650.89360.2891.4521-11.2242-40.6684-24.6053
171.1269-1.103-1.68544.61924.15575.6698-0.0024-0.25030.05620.17180.3131-0.33750.10870.5242-0.31070.31390.0427-0.0440.13850.01270.048438.386-63.0179-34.071
180.740.2755-0.23762.07091.03641.35580.0649-0.1642-0.03330.39250.005-0.02720.33670.0968-0.070.3280.0415-0.00060.07670.03050.025631.9726-68.7011-36.2602
190.74650.1763-0.2550.295-0.13170.45320.016-0.0487-0.07820.0656-0.02730.01370.1695-0.01850.01120.32280.00530.00510.05610.00460.013526.0038-68.39-46.8481
200.51120.06940.10091.97192.11084.16840.0344-0.08170.00240.1671-0.04190.03720.1377-0.10770.00750.25710.01520.00880.03960.01220.007632.0651-62.2063-38.1895
210.3687-0.5346-0.31585.80044.06523.5414-0.03110.0386-0.05-0.2141-0.19290.4354-0.2166-0.32590.22390.2297-0.02360.04630.16170.00160.0907-1.8948-13.4368-2.817
220.3279-0.5283-0.38941.17040.8951.70160.0482-0.0233-0.04960.0651-0.19720.1685-0.0536-0.55450.1490.3432-0.02630.0620.3254-0.06250.03742.9641-11.691611.907
2333.83375.5124-5.917711.22244.35164.6967-0.18640.6191-0.11440.3323-0.17380.69620.1027-0.08150.36020.2432-0.02120.01760.15380.03210.0854-10.3266-40.7445-10.699
240.33040.26030.16370.38110.12190.5050.0159-0.0438-0.01450.0603-0.02920.07840.0342-0.07720.01330.26710.01880.04690.0875-0.00270.05027.7408-12.7763.46
250.79911.18770.80394.53822.85053.0604-0.12810.17360.0179-0.40870.14560.1499-0.31380.0968-0.01760.29650.051-0.02190.1120.01820.06278.664310.5628-25.9159
261.3906-0.786-1.75632.02660.62812.34840.09140.6224-0.3074-0.2855-0.42610.4297-0.1242-0.85350.33470.31480.1354-0.03830.4508-0.14250.16630.790211.6559-16.873
270.42910.11430.07990.2620.04230.6434-0.0108-0.01240.0096-0.01750.00320.087-0.0727-0.11970.00770.26980.03790.01790.0646-0.01210.0658.17516.9133-13.0893
280.57461.20491.47773.57583.44784.9071-0.0064-0.07120.0343-0.062-0.08240.1178-0.1177-0.17960.08880.21240.03960.01810.0361-0.00050.033811.45829.9427-17.3504
293.35663.16985.18376.86.150910.77990.19680.4947-0.3147-0.04510.4285-0.45650.37670.8038-0.62530.31-0.03380.07250.1661-0.03740.079540.68560.4542-38.5192
301.0073-0.07960.55490.9399-0.10710.4472-0.09170.21040.0804-0.19850.1099-0.0013-0.18170.2043-0.01820.3699-0.10840.04890.1408-0.02680.038139.457319.6826-22.7163
310.4599-0.04280.02010.26220.05670.66110.00340.05130.0225-0.00970.00220.0224-0.13240.0305-0.00560.3034-0.01880.01260.0296-0.00130.020233.006713.6109-17.9751
320.60840.1810.33921.63021.8943.94610.00130.0606-0.021-0.081-0.00770.0624-0.0616-0.09220.00640.2353-0.0190.01020.0210.00610.013537.28298.7169-25.0077
330.3307-0.11010.18922.13924.647912.2037-0.01480.0622-0.18230.18210.1431-0.08240.6860.4645-0.12830.23510.0410.02360.177-0.03380.17353.8486-23.6146-18.6594
340.42180.41240.58572.12410.46941.42880.01540.0685-0.07040.04560.1702-0.39560.06540.3565-0.18560.252-0.0235-0.01970.183-0.04950.112858.0608-5.0909-2.5032
350.2118-0.1172-0.00990.57660.04480.5398-0.0145-0.0043-0.00650.01420.0209-0.1093-0.01560.0961-0.00640.2532-0.0221-0.0020.0889-0.01030.026848.7395-2.4728-5.2534
360.6805-0.5117-0.72932.6112.56334.11170.0230.05130.0011-0.05560.0484-0.1252-0.04160.0761-0.07140.1976-0.0107-0.01390.0560.00880.012250.6547-11.1573-8.7321
376.07731.0852-3.34879.72281.83778.86960.10510.2578-0.31910.2331-0.12550.29110.3848-0.3620.02040.4502-0.00720.01610.0279-0.01190.040831.0691-44.2993-8.6407
380.99630.0278-0.04631.4360.77951.3805-0.0027-0.0126-0.1480.208-0.02110.04580.280.02110.02380.37590.01530.00010.08740.03310.036332.0469-25.532615.6248
390.2860.1129-0.02470.59620.12540.4169-0.0094-0.0603-0.05570.15290.0148-0.05140.04740.0414-0.00540.31220.0043-0.00540.07140.00980.012535.6869-18.20511.4044
400.359-0.0191-0.08441.50330.68891.11490.00990.033200.03960.0169-0.06770.08690.0612-0.02680.27180.00740.01120.06220.00840.005130.0027-23.79024.2675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 66
2X-RAY DIFFRACTION2A67 - 122
3X-RAY DIFFRACTION3A123 - 245
4X-RAY DIFFRACTION4A246 - 302
5X-RAY DIFFRACTION5B34 - 65
6X-RAY DIFFRACTION6B66 - 122
7X-RAY DIFFRACTION7B123 - 247
8X-RAY DIFFRACTION8B248 - 302
9X-RAY DIFFRACTION9C34 - 53
10X-RAY DIFFRACTION10C54 - 102
11X-RAY DIFFRACTION11C103 - 109
12X-RAY DIFFRACTION12C110 - 302
13X-RAY DIFFRACTION13D33 - 48
14X-RAY DIFFRACTION14D49 - 109
15X-RAY DIFFRACTION15D110 - 297
16X-RAY DIFFRACTION16D298 - 302
17X-RAY DIFFRACTION17E34 - 65
18X-RAY DIFFRACTION18E66 - 122
19X-RAY DIFFRACTION19E123 - 245
20X-RAY DIFFRACTION20E246 - 302
21X-RAY DIFFRACTION21F34 - 70
22X-RAY DIFFRACTION22F71 - 102
23X-RAY DIFFRACTION23F103 - 109
24X-RAY DIFFRACTION24F110 - 304
25X-RAY DIFFRACTION25G34 - 68
26X-RAY DIFFRACTION26G69 - 109
27X-RAY DIFFRACTION27G110 - 265
28X-RAY DIFFRACTION28G266 - 302
29X-RAY DIFFRACTION29H33 - 53
30X-RAY DIFFRACTION30H54 - 109
31X-RAY DIFFRACTION31H110 - 247
32X-RAY DIFFRACTION32H248 - 302
33X-RAY DIFFRACTION33I32 - 53
34X-RAY DIFFRACTION34I54 - 109
35X-RAY DIFFRACTION35I110 - 247
36X-RAY DIFFRACTION36I248 - 302
37X-RAY DIFFRACTION37J32 - 46
38X-RAY DIFFRACTION38J47 - 109
39X-RAY DIFFRACTION39J110 - 220
40X-RAY DIFFRACTION40J221 - 304

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more