[English] 日本語
Yorodumi
- PDB-5wna: Structure of antibody 3D3 bound to the central conserved region o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wna
TitleStructure of antibody 3D3 bound to the central conserved region of RSV G
Components
  • Major surface glycoprotein G
  • mAb 3D3 Fab heavy chain
  • mAb 3D3 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / RSV / glycoprotein / G glycoprotein / viral protein / viral attachment protein / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Assembly and release of respiratory syncytial virus (RSV) virions / Translation of respiratory syncytial virus mRNAs / Respiratory syncytial virus (RSV) attachment and entry / RSV-host interactions / Maturation of hRSV A proteins / adhesion receptor-mediated virion attachment to host cell / virus-mediated perturbation of host defense response / symbiont entry into host cell / host cell plasma membrane / virion membrane ...Assembly and release of respiratory syncytial virus (RSV) virions / Translation of respiratory syncytial virus mRNAs / Respiratory syncytial virus (RSV) attachment and entry / RSV-host interactions / Maturation of hRSV A proteins / adhesion receptor-mediated virion attachment to host cell / virus-mediated perturbation of host defense response / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular region / plasma membrane
Similarity search - Function
Major surface glycoprotein G / Pneumovirus attachment glycoprotein G / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major surface glycoprotein G
Similarity search - Component
Biological speciesHomo sapiens (human)
Human respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFedechkin, S.O. / George, N.L. / Wolff, J.T. / Kauvar, L.M. / DuBois, R.M.
CitationJournal: Sci Immunol / Year: 2018
Title: Structures of respiratory syncytial virus G antigen bound to broadly neutralizing antibodies.
Authors: Fedechkin, S.O. / George, N.L. / Wolff, J.T. / Kauvar, L.M. / DuBois, R.M.
History
DepositionJul 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
H: mAb 3D3 Fab heavy chain
L: mAb 3D3 Fab light chain
B: Major surface glycoprotein G
C: mAb 3D3 Fab heavy chain
D: mAb 3D3 Fab light chain
A: Major surface glycoprotein G


Theoretical massNumber of molelcules
Total (without water)107,1486
Polymers107,1486
Non-polymers00
Water2,432135
1
H: mAb 3D3 Fab heavy chain
L: mAb 3D3 Fab light chain
B: Major surface glycoprotein G


Theoretical massNumber of molelcules
Total (without water)53,5743
Polymers53,5743
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-38 kcal/mol
Surface area20430 Å2
MethodPISA
2
C: mAb 3D3 Fab heavy chain
D: mAb 3D3 Fab light chain
A: Major surface glycoprotein G


Theoretical massNumber of molelcules
Total (without water)53,5743
Polymers53,5743
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-39 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.620, 135.010, 73.780
Angle α, β, γ (deg.)90.000, 107.450, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain D and (resseq 1:13 or resseq 15:23 or (resid...
21(chain L and (resseq 1:13 or resseq 15:68 or resseq...
12(chain C and (resseq 1:2 or (resid 3 and (name...
22(chain H and (resseq 1:2 or (resid 3 and (name...
13(chain A and (resseq 162:187 or (resid 189 and (name...
23(chain B and (resseq 161:186 or resseq 188:189))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNLEULEU(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 131 - 13
121PROPROCYSCYS(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE15 - 2315 - 23
131ARGARGARGARG(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE2424
141GLNGLNGLYGLY(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 2111 - 211
151GLNGLNGLYGLY(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 2111 - 211
161GLNGLNGLYGLY(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 2111 - 211
171GLNGLNGLYGLY(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 2111 - 211
181GLNGLNGLYGLY(chain D and (resseq 1:13 or resseq 15:23 or (resid...DE1 - 2111 - 211
211GLNGLNLEULEU(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 131 - 13
221PROPROGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB15 - 6815 - 68
231PHEPHELEULEU(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB71 - 12471 - 124
241SERSERASNASN(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB126 - 209126 - 209
251ARGARGARGARG(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB210210
261GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
271GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
281GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
291GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
2101GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
2111GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
2121GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
2131GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
2141GLNGLNGLYGLY(chain L and (resseq 1:13 or resseq 15:68 or resseq...LB1 - 2111 - 211
112GLUGLUGLUGLU(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 21 - 2
122GLNGLNGLNGLN(chain C and (resseq 1:2 or (resid 3 and (name...CD33
132GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
142GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
152GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
162GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
172GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
182GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
192GLUGLULYSLYS(chain C and (resseq 1:2 or (resid 3 and (name...CD1 - 2251 - 225
212GLUGLUGLUGLU(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 21 - 2
222GLNGLNGLNGLN(chain H and (resseq 1:2 or (resid 3 and (name...HA33
232GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
242GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
252GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
262GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
272GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
282GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
292GLUGLUCYSCYS(chain H and (resseq 1:2 or (resid 3 and (name...HA1 - 2271 - 227
113ASPASPLYSLYS(chain A and (resseq 162:187 or (resid 189 and (name...AF162 - 1874 - 29
123ILEILEILEILE(chain A and (resseq 162:187 or (resid 189 and (name...AF18931
133ASNASNPROPRO(chain A and (resseq 162:187 or (resid 189 and (name...AF161 - 1903 - 32
143ASNASNPROPRO(chain A and (resseq 162:187 or (resid 189 and (name...AF161 - 1903 - 32
153ASNASNPROPRO(chain A and (resseq 162:187 or (resid 189 and (name...AF161 - 1903 - 32
163ASNASNPROPRO(chain A and (resseq 162:187 or (resid 189 and (name...AF161 - 1903 - 32
213ASNASNCYSCYS(chain B and (resseq 161:186 or resseq 188:189))BC161 - 1863 - 28
223ARGARGILEILE(chain B and (resseq 161:186 or resseq 188:189))BC188 - 18930 - 31

NCS ensembles :
ID
1
2
3

-
Components

#1: Antibody mAb 3D3 Fab heavy chain


Mass: 24778.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody mAb 3D3 Fab light chain


Mass: 23487.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Major surface glycoprotein G / Attachment glycoprotein G / Membrane-bound glycoprotein / mG


Mass: 5308.158 Da / Num. of mol.: 2
Fragment: Central conserved region of RSV G, UNP residues 161-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A / Strain: A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03423
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 23% PEG 3350, 0.05 M zinc acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11503 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2017 / Details: Pilatus3 S, 25Hz, S/N 60-0134
RadiationMonochromator: Si(111) Khozu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11503 Å / Relative weight: 1
ReflectionResolution: 2.4→48.72 Å / Num. obs: 46906 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 35.45 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.05 / Rrim(I) all: 0.126 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.485.60.84446170.670.3860.93199
9.3-48.727.10.0358260.9990.0140.03899.3

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I30

5i30


Resolution: 2.4→48.719 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.43 / Details: PHENIX
RfactorNum. reflection% reflection
Rfree0.2455 2000 4.27 %
Rwork0.1915 --
obs0.1938 46868 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.5 Å2 / Biso mean: 41.9572 Å2 / Biso min: 17.96 Å2
Refinement stepCycle: final / Resolution: 2.4→48.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7120 0 0 135 7255
Biso mean---38.59 -
Num. residues----934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067326
X-RAY DIFFRACTIONf_angle_d0.9359981
X-RAY DIFFRACTIONf_chiral_restr0.051118
X-RAY DIFFRACTIONf_plane_restr0.0071281
X-RAY DIFFRACTIONf_dihedral_angle_d15.734385
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D1910X-RAY DIFFRACTION10.278TORSIONAL
12L1910X-RAY DIFFRACTION10.278TORSIONAL
21C1929X-RAY DIFFRACTION10.278TORSIONAL
22H1929X-RAY DIFFRACTION10.278TORSIONAL
31A250X-RAY DIFFRACTION10.278TORSIONAL
32B250X-RAY DIFFRACTION10.278TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.35461420.28013196333899
2.46-2.52660.32741400.26033130327099
2.5266-2.60090.2931430.252932203363100
2.6009-2.68480.32631430.231432013344100
2.6848-2.78080.28891420.221732043346100
2.7808-2.89210.30531430.21631923335100
2.8921-3.02370.28791440.21332153359100
3.0237-3.18310.27841420.20543192333499
3.1831-3.38250.24151430.201332183361100
3.3825-3.64360.23651430.173832033346100
3.6436-4.01010.26491430.172432203363100
4.0101-4.590.18961440.154432253369100
4.59-5.78140.18521430.16613209335299
5.7814-48.72950.20471450.17933243338899
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)
11.9818-2.2052-0.13292.7740.29493.81210.28590.10890.2171-1.003-0.2749-0.46470.25660.274-0.02030.35790.04750.02850.32490.12810.304244.593612.964370.2317
22.1108-0.1975-0.40562.6240.05934.53080.33070.14050.0682-0.6536-0.08870.20890.0886-0.2286-0.25110.41730.005-0.05880.22570.06020.238334.331412.926771.1538
33.2029-3.402-0.40565.70262.77993.46650.25830.0896-0.0469-0.9864-0.49870.0907-0.6221-0.03690.30770.4097-0.0098-0.02190.26290.07390.350637.502420.848773.663
41.8092-1.31310.0294.80193.15233.9530.26220.1634-0.2514-0.3113-0.2640.27520.7759-0.1801-0.04170.5723-0.0137-0.10480.29010.00540.219537.3946-1.088372.4798
54.25582.90213.69091.9592.64525.23640.10850.00790.2513-0.0856-0.1806-0.3968-0.24530.00380.04250.338-0.0487-0.06080.21550.09240.38646.267324.134484.5567
66.6066-1.3949-1.66496.74324.30753.2381-0.587-0.97930.03281.59050.00790.0081.0480.21220.1520.43-0.172-0.05870.55340.00580.371754.538220.2655113.4483
73.8721-0.64471.79184.3598-1.58084.321-0.0986-0.22130.04140.1952-0.0331-0.16080.01070.14220.16270.1968-0.0572-0.0240.26940.01370.252453.075718.3071101.8087
87.9131-3.97557.26614.8165-6.60849.8512-0.02370.407-0.24110.011-0.2463-0.5161-0.13351.48370.18670.2775-0.0421-0.02010.3793-0.01250.322461.230119.766699.2022
96.8356-1.13830.44053.7994-4.08087.7418-0.0617-0.40830.33890.21730.0010.0511-0.30460.76750.38330.1924-0.124-0.02470.3012-0.00260.38661.72424.7642105.4294
105.3543-2.28734.56122.0058-1.72825.3592-0.0111-0.21440.071-0.09380.05290.26840.2055-0.26080.04780.2721-0.09680.03840.32860.04670.437729.7128-1.937693.1321
112.0642-1.9616-0.03183.6035-1.97223.6640.26410.113-0.1205-0.4368-0.06280.42170.3726-0.2578-0.1480.2662-0.0477-0.11050.27010.0010.343333.4384-4.508382.5616
120.0716-0.4282-0.55634.7434-1.87834.37540.1044-0.0228-0.1759-0.40470.07870.22410.2447-0.3629-0.14670.2591-0.0878-0.11130.26840.02070.391531.2235-3.007985.1164
130.94130.53782.35480.43450.95626.85-0.09130.0629-0.0632-0.16040.1112-0.1703-0.0616-0.17640.08960.3612-0.0822-0.00760.33970.10680.304238.80610.1757105.2072
141.8559-1.0021-0.7929.5138-5.52618.5296-0.0452-0.26370.29820.10670.1755-0.4234-0.31840.323-0.06290.2522-0.0276-0.05470.3072-0.09280.28851.421427.2195111.5138
151.7084-0.7536-0.52596.66191.16291.8984-0.1319-0.39740.10570.07310.12570.03670.1363-0.17980.05310.2001-0.0502-0.01910.41420.0120.23139.822918.4191112.0287
161.7638-1.8624-0.49574.16460.67211.2999-0.1009-0.40160.10260.18290.17770.01790.0446-0.0264-0.06260.192-0.069-0.02930.4177-0.00430.294342.280919.7477112.2445
172.42880.5293-2.97816.6813-2.3174.08230.71660.985-0.3147-1.1471-0.6530.71190.0018-0.3774-0.12640.67350.0424-0.31310.41410.03870.511525.70883.365665.2542
180.0599-0.0841-0.3010.06960.33211.03080.53580.5216-0.2481-0.5689-0.45270.36810.58690.1288-0.06170.8180.1517-0.21530.4907-0.08590.322838.638-9.209460.8257
195.05160.8016-3.25330.316-0.93073.01870.6111.09240.5010.4487-0.17040.1948-0.7253-0.41060.99341.24630.289-0.50510.5189-0.11890.225935.5779-9.523557.3049
205.132-4.20831.57478.5248-5.4145.33480.0054-0.152-0.2214-0.85180.05550.3694-0.0574-0.44530.00020.27940.0265-0.03830.2808-0.09320.241149.385-29.626473.9593
215.61760.20770.09260.4493-0.03833.74630.25080.63330.0661-1.121-0.02770.483-0.2954-0.374-0.27020.55590.0483-0.06240.3903-0.00540.249249.8565-19.160264.9936
224.07150.6806-2.58034.3734-1.28586.01230.40150.0233-0.1659-0.6251-0.2481-0.1262-0.2980.4147-0.07480.38990.00860.03640.2032-0.01170.225259.5237-21.654672.7898
230.774-1.14460.39986.5405-1.26672.70790.22340.2244-0.0036-0.5887-0.1822-0.3521-0.22770.2728-0.00560.34590.02170.03030.29440.02030.26158.1543-21.415470.0282
241.11621.5118-1.93483.7032-2.29893.2676-0.0452-0.0619-0.1724-0.3769-0.076-0.06780.3948-0.09480.13680.2755-0.005-0.07980.2493-0.00590.266849.2874-32.356281.9646
254.6368-2.07070.02076.9597-3.35541.8315-0.0972-1.18780.22091.6616-0.11450.4114-0.1814-0.70520.1970.4084-0.06080.0760.5831-0.07220.330840.6418-33.2084112.1792
263.01611.4568-0.23022.93810.22023.6986-0.0833-0.28350.1946-0.1144-0.1310.3491-0.1722-0.33810.1620.1260.0253-0.02350.27270.01280.265842.4651-30.9051100.1404
276.72880.4129-3.70575.87722.55083.3840.03060.03810.30970.0533-0.4880.6081-0.2829-1.2110.53940.21430.0085-0.0660.3787-0.04280.347133.3675-34.2303100.4982
287.1569-3.2711-4.58744.15472.36425.09510.06590.0402-0.2583-0.01750.054-0.6119-0.24670.1707-0.1340.1976-0.0835-0.07780.3131-0.04930.411964.92-9.942592.5524
291.33-0.7283-0.16522.33821.31052.90350.1024-0.0526-0.1123-0.5027-0.1635-0.6197-0.33780.43210.01910.2894-0.08270.10230.32240.01950.366461.2118-7.038482.0471
300.5042-1.1711-0.23782.79031.2584.47370.1091-0.04430.0647-0.22140.0478-0.412-0.38490.3422-0.09140.2452-0.08760.06740.2928-0.02380.439461.899-5.793587.6523
310.85360.56670.78944.3920.56314.28910.41640.0443-0.0491-0.51830.365-0.5798-0.33810.5828-0.47610.3412-0.10970.11930.3213-0.05620.374166.7422-15.748876.1338
323.32870.1535-3.16411.0353-0.72993.5187-0.321-0.08550.02920.66320.6676-0.2218-0.04080.252-0.21490.2917-0.1094-0.02810.2347-0.10780.326956.2866-12.5801104.6235
331.97050.7960.84137.6256-0.31053.8316-0.1219-0.2197-0.12890.11340.16720.05450.1408-0.0495-0.07490.21150.01310.00590.31520.01970.268348.2854-33.0834108.9589
342.2823-3.5592-0.47919.2756-1.69811.37-0.1775-0.2757-0.07850.04210.17650.0144-0.0110.1420.05360.1775-0.0361-0.01590.31850.01010.293555.0288-28.8342107.6457
351.49760.82631.31898.98240.01122.6283-0.0017-0.3948-0.25880.73560.1136-0.06410.2418-0.0981-0.08650.18660.01770.05310.41280.08650.314553.1741-36.9899114.9681
363.7902-2.38533.03692.6995-3.56424.69431.10720.33480.1051-1.7958-0.6146-1.34710.09581.0964-0.48970.71810.03860.13830.5780.05730.509271.3573-18.558763.9793
371.98-2.36441.314.6106-1.76566.99840.42720.08190.3894-0.9519-0.3315-0.8702-0.63350.65370.23980.7880.0090.46410.46430.20030.314362.4905-8.844463.7746
382.12610.36120.19511.25930.21320.04720.38780.86710.29-0.499-0.1110.0163-0.26550.4045-0.18310.79510.09960.04820.39910.14110.373652.09872.043459.3072
395.04660.8207-0.14076.7564-0.38370.0146-0.06511.0040.0417-1.69890.0708-0.2739-0.5550.65350.01290.91930.07070.15380.48970.10880.385658.0426-0.25557.1369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 33 )H1 - 33
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 76 )H34 - 76
3X-RAY DIFFRACTION3chain 'H' and (resid 77 through 91 )H77 - 91
4X-RAY DIFFRACTION4chain 'H' and (resid 92 through 114 )H92 - 114
5X-RAY DIFFRACTION5chain 'H' and (resid 115 through 130 )H115 - 130
6X-RAY DIFFRACTION6chain 'H' and (resid 131 through 145 )H131 - 145
7X-RAY DIFFRACTION7chain 'H' and (resid 146 through 201 )H146 - 201
8X-RAY DIFFRACTION8chain 'H' and (resid 202 through 214 )H202 - 214
9X-RAY DIFFRACTION9chain 'H' and (resid 215 through 227 )H215 - 227
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 18 )L1 - 18
11X-RAY DIFFRACTION11chain 'L' and (resid 19 through 61 )L19 - 61
12X-RAY DIFFRACTION12chain 'L' and (resid 62 through 100 )L62 - 100
13X-RAY DIFFRACTION13chain 'L' and (resid 101 through 112 )L101 - 112
14X-RAY DIFFRACTION14chain 'L' and (resid 113 through 127 )L113 - 127
15X-RAY DIFFRACTION15chain 'L' and (resid 128 through 154 )L128 - 154
16X-RAY DIFFRACTION16chain 'L' and (resid 155 through 211 )L155 - 211
17X-RAY DIFFRACTION17chain 'B' and (resid 161 through 168 )B161 - 168
18X-RAY DIFFRACTION18chain 'B' and (resid 169 through 179 )B169 - 179
19X-RAY DIFFRACTION19chain 'B' and (resid 180 through 190 )B180 - 190
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 17 )C1 - 17
21X-RAY DIFFRACTION21chain 'C' and (resid 18 through 33 )C18 - 33
22X-RAY DIFFRACTION22chain 'C' and (resid 34 through 57 )C34 - 57
23X-RAY DIFFRACTION23chain 'C' and (resid 58 through 112 )C58 - 112
24X-RAY DIFFRACTION24chain 'C' and (resid 113 through 130 )C113 - 130
25X-RAY DIFFRACTION25chain 'C' and (resid 131 through 145 )C131 - 145
26X-RAY DIFFRACTION26chain 'C' and (resid 146 through 199 )C146 - 199
27X-RAY DIFFRACTION27chain 'C' and (resid 200 through 225 )C200 - 225
28X-RAY DIFFRACTION28chain 'D' and (resid 1 through 18 )D1 - 18
29X-RAY DIFFRACTION29chain 'D' and (resid 19 through 61 )D19 - 61
30X-RAY DIFFRACTION30chain 'D' and (resid 62 through 90 )D62 - 90
31X-RAY DIFFRACTION31chain 'D' and (resid 91 through 100 )D91 - 100
32X-RAY DIFFRACTION32chain 'D' and (resid 101 through 112 )D101 - 112
33X-RAY DIFFRACTION33chain 'D' and (resid 113 through 143 )D113 - 143
34X-RAY DIFFRACTION34chain 'D' and (resid 144 through 173 )D144 - 173
35X-RAY DIFFRACTION35chain 'D' and (resid 174 through 211 )D174 - 211
36X-RAY DIFFRACTION36chain 'A' and (resid 161 through 165 )A161 - 165
37X-RAY DIFFRACTION37chain 'A' and (resid 166 through 173 )A166 - 173
38X-RAY DIFFRACTION38chain 'A' and (resid 174 through 180 )A174 - 180
39X-RAY DIFFRACTION39chain 'A' and (resid 181 through 190 )A181 - 190

+
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