[English] 日本語
Yorodumi
- PDB-4p2q: Crystal structure of the 5cc7 TCR in complex with 5c2/I-Ek -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p2q
TitleCrystal structure of the 5cc7 TCR in complex with 5c2/I-Ek
Components
  • (5cc7 T-cell receptor ...) x 2
  • 5c2 peptide
  • H-2 class II histocompatibility antigen, E-K alpha chain
  • MHC class II E-beta-k
KeywordsIMMUNE SYSTEM / T cell receptor / peptide-MHC complex
Function / homology
Function and homology information


immunoglobulin mediated immune response / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / MHC class II protein complex binding / late endosome membrane / adaptive immune response ...immunoglobulin mediated immune response / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / lysosomal membrane / external side of plasma membrane / plasma membrane
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class II histocompatibility antigen, E-K alpha chain / MHC class II antigen IEk-beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBirnbaum, M.E. / Ozkan, E. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Cell / Year: 2014
Title: Deconstructing the Peptide-MHC Specificity of T Cell Recognition.
Authors: Birnbaum, M.E. / Mendoza, J.L. / Sethi, D.K. / Dong, S. / Glanville, J. / Dobbins, J. / Ozkan, E. / Davis, M.M. / Wucherpfennig, K.W. / Garcia, K.C.
History
DepositionMar 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Feb 25, 2015Group: Derived calculations
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag ..._entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.8Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.9Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 class II histocompatibility antigen, E-K alpha chain
B: MHC class II E-beta-k
C: 5c2 peptide
D: 5cc7 T-cell receptor alpha chain
E: 5cc7 T-cell receptor beta chain
F: H-2 class II histocompatibility antigen, E-K alpha chain
G: MHC class II E-beta-k
H: 5c2 peptide
I: 5cc7 T-cell receptor alpha chain
J: 5cc7 T-cell receptor beta chain
K: H-2 class II histocompatibility antigen, E-K alpha chain
L: MHC class II E-beta-k
M: 5c2 peptide
N: 5cc7 T-cell receptor alpha chain
O: 5cc7 T-cell receptor beta chain
P: H-2 class II histocompatibility antigen, E-K alpha chain
Q: MHC class II E-beta-k
R: 5c2 peptide
S: 5cc7 T-cell receptor alpha chain
T: 5cc7 T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,87225
Polymers407,76620
Non-polymers1,1065
Water00
1
A: H-2 class II histocompatibility antigen, E-K alpha chain
B: MHC class II E-beta-k
C: 5c2 peptide
D: 5cc7 T-cell receptor alpha chain
E: 5cc7 T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3847
Polymers101,9415
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: H-2 class II histocompatibility antigen, E-K alpha chain
G: MHC class II E-beta-k
H: 5c2 peptide
I: 5cc7 T-cell receptor alpha chain
J: 5cc7 T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1636
Polymers101,9415
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: H-2 class II histocompatibility antigen, E-K alpha chain
L: MHC class II E-beta-k
M: 5c2 peptide
N: 5cc7 T-cell receptor alpha chain
O: 5cc7 T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3847
Polymers101,9415
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: H-2 class II histocompatibility antigen, E-K alpha chain
Q: MHC class II E-beta-k
R: 5c2 peptide
S: 5cc7 T-cell receptor alpha chain
T: 5cc7 T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)101,9415
Polymers101,9415
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)262.900, 102.210, 214.110
Angle α, β, γ (deg.)90.00, 95.04, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE BIOLOGICAL ASSEMBLY WAS DETERINED BY SURFACE PLASMA RESONANCE

-
Components

-
Protein , 2 types, 8 molecules AFKPBGLQ

#1: Protein
H-2 class II histocompatibility antigen, E-K alpha chain


Mass: 23618.467 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04224
#2: Protein
MHC class II E-beta-k


Mass: 24433.174 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Eb1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31163

-
5cc7 T-cell receptor ... , 2 types, 8 molecules DINSEJOT

#4: Protein
5cc7 T-cell receptor alpha chain


Mass: 22765.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#5: Protein
5cc7 T-cell receptor beta chain


Mass: 29647.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

-
Protein/peptide / Sugars , 2 types, 9 molecules CHMR

#3: Protein/peptide
5c2 peptide


Mass: 1477.622 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium citrate, 18% PEG 3350, 4% tert-butanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2013
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.3→39.63 Å / Num. obs: 84684 / % possible obs: 99.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 9.3
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.98 / Mean I/σ(I) obs: 1 / % possible all: 96.5

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→39.63 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 4232 5 %
Rwork0.1881 --
obs0.1905 84684 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25597 0 70 0 25667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00526344
X-RAY DIFFRACTIONf_angle_d0.88835766
X-RAY DIFFRACTIONf_dihedral_angle_d12.9969428
X-RAY DIFFRACTIONf_chiral_restr0.0373877
X-RAY DIFFRACTIONf_plane_restr0.0044717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.33760.40121270.36772376X-RAY DIFFRACTION90
3.3376-3.37680.38331310.30992709X-RAY DIFFRACTION100
3.3768-3.4180.30091340.28622694X-RAY DIFFRACTION100
3.418-3.46120.31821240.30892651X-RAY DIFFRACTION99
3.4612-3.50680.29031540.27172657X-RAY DIFFRACTION99
3.5068-3.55480.32411420.26122656X-RAY DIFFRACTION99
3.5548-3.60550.32261440.26412627X-RAY DIFFRACTION98
3.6055-3.65930.34311040.26332713X-RAY DIFFRACTION100
3.6593-3.71640.35371180.28922706X-RAY DIFFRACTION99
3.7164-3.77730.25911400.23062696X-RAY DIFFRACTION100
3.7773-3.84240.2961440.2092644X-RAY DIFFRACTION100
3.8424-3.91220.26911530.22122713X-RAY DIFFRACTION99
3.9122-3.98740.25771410.20652650X-RAY DIFFRACTION100
3.9874-4.06870.23681450.18762672X-RAY DIFFRACTION100
4.0687-4.15710.23021570.1842720X-RAY DIFFRACTION100
4.1571-4.25370.20881440.1732700X-RAY DIFFRACTION100
4.2537-4.35990.26831320.15832657X-RAY DIFFRACTION100
4.3599-4.47760.15821660.14242651X-RAY DIFFRACTION98
4.4776-4.60920.1621100.12782698X-RAY DIFFRACTION100
4.6092-4.75780.17641520.12852687X-RAY DIFFRACTION100
4.7578-4.92750.19061500.13162727X-RAY DIFFRACTION100
4.9275-5.12440.12561170.13442711X-RAY DIFFRACTION100
5.1244-5.35710.19671640.14432683X-RAY DIFFRACTION100
5.3571-5.63880.22171530.15762739X-RAY DIFFRACTION100
5.6388-5.9910.24641520.18262635X-RAY DIFFRACTION99
5.991-6.45170.25151450.18712723X-RAY DIFFRACTION100
6.4517-7.09760.24821450.17942716X-RAY DIFFRACTION100
7.0976-8.1170.21771570.16992716X-RAY DIFFRACTION100
8.117-10.19780.22751430.16372744X-RAY DIFFRACTION99
10.1978-39.67660.25611440.2242781X-RAY DIFFRACTION99
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)
15.11911.7289-0.75022.91240.1762.40470.2389-0.2764-0.2374-0.1032-0.22380.42270.11630.30540.1450.63280.09990.06720.43350.09870.58261.2102-8.4862255.6182
27.53322.3738-0.38046.1326-1.81433.1466-0.12560.9198-1.0939-0.82560.1375-0.76350.064-0.3395-0.01690.73470.09870.03560.6373-0.19730.792459.0428-15.3801246.4415
32.2474-1.5212-1.94375.262.40052.1331-0.20930.11180.6475-0.34970.215-1.0158-0.83770.11280.07310.60250.00890.0110.65270.10350.695671.82482.7101255.6918
42.1653-0.89680.37292.42950.26591.2932-0.0871-0.1945-0.975-0.19260.04150.18230.13040.1599-0.02640.72450.16650.15940.54320.10421.242671.5572-23.7714259.5542
53.60890.4480.50534.60881.43652.32790.279-0.58-1.21470.1295-0.4025-1.27250.2246-0.1206-0.13910.71710.18690.12880.67370.111.339279.3396-27.8461264.0998
63.07272.63370.21023.2513-0.20071.9754-0.8104-0.62040.22120.11990.433-0.0674-0.15610.25830.17150.63670.07-0.01550.39820.1240.683265.0679-3.2829260.1246
70.7327-1.4099-0.28811.96650.28782.30820.0484-0.52040.29130.30140.03250.6586-0.1498-0.0775-0.0220.76120.12550.07020.44230.07780.802255.98372.0984263.4983
84.92250.3591-0.080.6398-1.50873.1871-0.16140.0620.28360.19480.31740.172-0.44820.00190.12430.76180.1683-0.01040.51910.080.833554.642910.5556257.0927
90.5927-1.5089-0.22244.5393-1.42952.7406-0.1637-0.0758-0.9776-0.42960.30120.65970.0189-0.6863-0.22120.7258-0.0362-0.0310.43650.07851.19746.693-16.6908253.6571
103.5911-0.76891.08444.65952.01141.3492-0.4102-1.332-2.25851.4441-1.8299-0.20481.36810.9776-0.34661.28640.65690.2165-0.5661.25472.053457.6447-37.7772268.7671
112.39551.53360.15753.1068-0.57883.702-0.2078-0.72490.27280.3918-0.64070.28090.4535-0.21030.7830.8620.01160.27530.8260.16771.141253.7296-30.0395271.3772
120.14280.8652-0.4014.1878-2.01881.11570.9215-1.86291.77771.9776-0.30161.0952-0.554-0.5558-0.34691.612-0.20740.13810.93210.43391.207954.5535-35.1122273.6796
132.5467-2.43090.93779.7717-4.05814.68380.4549-1.49130.72910.40830.20230.10941.0636-1.2966-0.47071.1797-0.23220.14711.06850.45631.843347.0605-39.1618268.0849
145.60141.6636-0.32993.8006-0.21613.79790.03631.07610.2959-0.87-0.33110.39-0.6942-0.0484-0.15670.5730.0631-0.07430.63620.07440.602256.91570.8798248.237
155.0952-0.13820.56943.2462-2.15993.17750.06790.1664-0.0598-0.01240.01770.0223-0.1399-0.31440.00970.74620.2180.03380.66860.02480.560938.314612.2846238.8202
165.7638-4.44094.50824.2606-4.17494.0908-0.01441.44061.2796-0.0654-0.07970.40230.1293-0.4164-0.25151.0320.37230.08961.37080.46781.027324.044128.043227.7396
172.87931.34750.15181.5879-0.48263.1794-0.14011.0226-0.0465-0.3794-0.20190.2167-0.2476-0.58750.19751.24480.47480.01251.58520.23391.407826.878735.6615213.8733
183.2442-1.26570.37543.0314-2.12333.79790.04710.6099-0.0364-0.0694-0.1627-0.2516-0.19370.30060.06780.82960.18690.08380.88710.05360.57759.052817.494228.2958
194.1326-0.0078-1.97452.4645-0.00582.70180.51660.63880.7131-0.2023-0.15840.2836-0.5129-0.0094-0.22321.27660.35450.16271.44630.4670.885342.741239.9381217.6939
203.5041-1.43960.12711.9735-0.35250.7450.0262-0.7490.15150.38060.0433-0.2184-0.3165-0.0632-0.15741.05780.06170.07960.83980.00090.606162.71576.1458291.9286
210.67382.2498-0.69317.1439-2.08980.51780.29950.119-0.92591.5231-0.777-2.0176-0.56621.05820.11280.7861-0.21660.011.6516-0.30011.530783.34590.2215281.9085
221.86050.8782-0.09383.9467-1.93342.38030.2013-0.45920.46560.35340.11-0.3455-0.63410.4417-0.29871.2054-0.24050.16840.9085-0.25811.16976.015524.5233287.7508
232.7095-2.67812.38184.3588-0.71543.27680.2262-0.5373-0.58290.34710.02350.1549-0.69270.5777-0.09050.742-0.04670.01170.8802-0.03350.73268.36622.6033283.4973
246.7943-1.42621.55021.9407-0.25623.41690.58481.6722-0.08340.0493-0.55950.59290.08590.4483-0.30050.83320.02120.1120.64690.05780.567457.10671.3344277.8086
254.13063.4146-1.89065.32731.29623.51790.0213-0.4815-0.6802-0.04750.0972-0.6542-0.11030.2817-0.05430.67320.06860.02110.5309-0.00510.740765.3447-9.2752277.9118
264.4634-4.7679-0.73347.23630.71381.9564-0.2155-0.0445-0.12590.43760.86520.4508-0.3845-0.8635-0.15020.75450.0999-0.10210.55140.00680.534551.4785-9.2471283.1846
272.912-1.41970.17642.7545-1.3130.90280.20830.12381.14250.43470.4010.6266-0.7603-0.2548-0.35521.32510.05920.17110.6257-0.06931.084353.793524.8794278.7932
281.6008-0.3728-0.0361.90460.08720.41480.80170.52870.7878-1.2076-0.391-0.0663-0.13840.0449-0.26251.51520.1330.38250.73070.12871.295758.448333.4477271.5551
292.082-0.51791.4151.6942-1.37682.4764-0.5255-0.8045-0.47561.37010.20870.78410.4818-0.30560.04540.91510.24570.07670.86610.09760.953857.4676-3.1569291.7463
303.87531.9507-0.77052.4979-1.76162.97130.3226-0.0748-0.32410.08920.12640.09770.0708-0.3947-0.32420.89310.12930.06140.8260.2280.934935.6329-18.2052294.1852
311.2959-0.14130.1510.9981-0.03491.5872-0.1489-0.4977-0.44080.31110.19280.5884-0.04-0.7729-0.07661.5095-0.181-0.03481.52050.4541.846719.8411-41.6279311.9304
321.21781.0969-0.95314.2291-1.72432.76670.0789-0.2466-0.06080.34590.00340.16090.17310.2654-0.05180.98780.040.00320.89560.24860.727154.2959-21.8416309.6822
333.95440.31671.54472.6015-0.14553.75240.3265-0.2943-0.5331-0.21770.17440.49620.65190.0629-0.28841.4428-0.0906-0.03191.02920.330.991336.2323-45.5153313.1169
343.1681.06740.0542.6530.20391.7297-0.10840.24640.5623-0.11-0.16630.5423-0.3267-0.19210.11540.6380.2686-0.04080.94810.07020.9922-12.420120.0194252.8824
352.1314-0.8265-0.76912.85720.55744.0623-0.53791.3592-1.3691-0.6830.39291.28920.173-0.5580.2870.75110.3913-0.0971.22040.08911.3486-23.42187.1459243.2666
362.9308-0.2385-0.40271.39-0.27711.4573-0.0453-0.36990.1935-0.03790.24270.097-0.28950.1667-0.17790.7490.24790.04580.99220.02721.2518-26.822523.8574263.831
376.4432-2.06810.68773.74990.34422.9874-0.6159-1.2208-0.11240.9072-0.41191.91380.2549-0.66080.3830.89130.38220.15141.26410.09321.3183-35.914424.7054267.5634
389.78061.49813.98571.52820.90043.2071-0.2412-0.21320.03550.10720.1991.1213-0.1507-0.2891-0.09780.62460.1533-0.08911.0721-0.12161.0981-18.39227.783252.178
391.70340.43570.04721.35120.17880.94590.98780.6732-1.27720.2439-0.2290.1430.55320.1911-0.42390.79130.2891-0.22440.9751-0.11991.1678-10.1410.6826253.0858
401.2605-1.09970.02421.59630.05161.1779-0.5340.1781-0.4947-1.3618-0.31790.07870.4423-0.01340.45260.90590.3389-0.21751.5056-0.40121.4042-13.4432-5.4741241.7234
412.18522.17171.47474.33811.26491.40240.42990.27950.1932-0.8036-0.2909-1.1517-0.26930.34880.12990.65440.2605-0.03421.0641-0.34431.18220.07122.7155244.747
420.816-1.409-1.21145.07090.48282.7247-0.51990.25870.56650.11680.3512-0.2196-0.58210.5677-0.10990.82640.2206-0.06191.04630.04481.07741.685416.2601256.0171
434.12451.0537-2.87780.4563-0.80052.3381-0.1827-1.29320.18070.4269-0.3404-0.16980.0826-1.29730.44690.96620.2858-0.00461.7113-0.28490.6317-11.55225.993277.3063
444.4092-0.1252-0.28074.8448-1.24540.79470.6308-1.4968-0.8751.3255-0.4781-0.8519-0.1621-1.12530.00761.13530.2812-0.03952.23110.32991.072-9.167918.9466282.1477
451.40040.6962-0.36721.12830.23970.2849-0.7357-0.7573-1.6233-1.15990.48130.5431-0.22840.45730.14632.402-0.28230.11692.53040.38641.4563-15.045215.2683292.9141
462.47180.40951.33523.44750.850.91171.3268-1.12260.3030.6606-0.33691.84520.86610.6798-0.43920.92960.15770.23161.7992-0.10660.7694-15.114621.2655279.7346
472.7594-0.4174-0.89233.03471.2414.3990.8063-0.6649-0.95310.2385-0.86141.3220.57820.406-0.40521.2110.1550.01132.4296-0.18281.0586-6.675826.9138286.5553
483.09930.2921.93713.95851.80874.63060.1110.6133-0.1532-0.33760.7119-0.2967-0.3318-0.4285-0.49310.79770.2788-0.0191.26350.02591.1674-7.076212.6321243.6134
493.06660.3723-1.53281.425-0.25282.93430.05290.2609-0.6352-0.2004-0.17510.2296-0.2598-0.20470.07560.79230.2805-0.12321.0829-0.0680.815114.02318.4235233.5604
501.70430.0735-0.26320.73290.95261.5371-0.24050.9559-0.8686-0.4165-0.14110.0125-1.0088-0.85290.35231.13640.21530.08131.5822-0.29970.827532.09793.9665206.7339
513.1308-0.18330.74221.9477-0.19973.3556-0.58341.04140.2048-0.0570.2199-0.2943-0.7616-1.15970.39081.30170.14270.02661.7191-0.24881.229233.75448.7505205.0576
520.82250.4546-1.93071.3385-0.57923.6828-0.01310.97440.0397-0.54620.1820.5414-0.2485-0.881-0.03811.01970.3869-0.25121.921-0.08021.0784-2.865914.5002217.7412
534.25-0.0710.89243.02970.00292.35970.14431.9058-0.5541-0.6588-0.20160.3985-0.1204-0.95620.09371.13950.1494-0.1092.3199-0.28690.933217.56514.1876199.0005
542.9722-0.00251.53192.2383-0.22561.5496-0.04380.2751-0.2199-0.27080.4458-0.20170.3825-0.4856-0.34070.86440.0839-0.26730.8752-0.10431.3923-4.1829-17.014261.7613
554.0325-0.9509-1.42190.93790.4192.46370.04010.23550.84760.2620.9913-0.72131.7884-0.5555-0.89941.072-0.0217-0.54121.09830.16811.8178-13.6069-22.0875264.8178
564.4812-2.3564-1.35861.10240.66313.2496-0.1348-0.1852-1.47230.2211-0.04910.57960.492-0.14170.06021.15950.0095-0.24410.85710.18551.9605-8.785-24.6271268.1267
571.2057-0.12491.5854-0.0587-0.02591.9240.1425-0.39410.1178-0.57380.680.59240.7971-0.6379-0.55280.79340.0028-0.35431.1439-0.13042.4169-26.3346-8.3527260.5329
581.51170.42970.26440.1585-0.15880.9332-0.6175-0.0349-1.0025-1.59020.60640.74820.397-1.1304-0.09461.5366-0.1192-0.17781.3215-0.47711.5105-10.169-31.6992238.7323
591.6699-0.6519-1.81820.8540.63073.0958-0.0610.1993-0.4669-0.13450.89280.53111.9451-0.1382-0.60131.49860.0002-0.69441.3973-0.43782.2056-18.4358-26.124248.8717
604.88241.98135.03290.85812.25085.58371.0508-0.5992-0.9741-0.9015-0.78481.23780.5912-0.1325-0.61571.71820.0209-0.30891.4554-0.20352.4409-21.9161-37.7708247.9062
611.32680.89762.00168.83364.02566.49290.65470.713-0.3669-0.1919-0.3104-0.06280.9694-0.28680.24751.29130.0832-0.36071.2241-0.35431.998-16.0283-27.254247.5468
623.4593-2.086-4.19993.9653.40585.30231.03141.4155-0.15410.0801-0.4990.68950.9172-0.9772-0.6431.4345-0.074-0.44591.779-0.12752.1116-24.4779-23.8692243.0939
633.584-1.4749-0.32693.23420.93951.02690.06450.5935-0.7293-0.1512-0.17160.24810.17590.01150.01150.85170.1388-0.11470.983-0.03511.1366-7.0205-11.1389263.4088
642.87610.95711.13772.5020.80992.6661-0.0083-0.3831-0.2-0.16930.05030.3674-0.0041-0.40140.05450.99950.27280.01660.95680.1391.3747-9.6722-2.0566270.6778
651.47460.0414-0.01860.33510.85422.5490.43080.4442-0.9769-0.35640.2657-0.18650.3840.9288-0.55481.20990.3107-0.22341.1846-0.31391.64464.8443-20.2677252.6626
662.0347-0.81210.8470.57680.31591.11031.1030.41540.5474-0.810.1962-0.81230.36810.6191-0.67491.6590.4831-0.01411.7503-0.30411.73093.6456-22.3952233.7764
675.9196-1.241-2.11954.54571.82915.7988-0.79330.5882-1.02531.27150.80670.27350.75-0.3863-0.40480.87940.06240.03540.78130.17041.586-3.9968-18.4001274.4479
682.6141-0.96081.09930.8505-0.86032.88920.4844-0.5987-0.5026-0.0043-0.2550.47190.4369-0.3171-0.08380.9010.05070.00080.97090.29651.016114.7989-16.984291.4357
694.07480.1824-0.323.5436-0.08792.9422-0.2313-1.2023-0.01591.2211-0.26251.0725-0.0046-1.27510.06671.192-0.04170.34031.22370.18371.30816.4127-10.2106297.5147
702.84040.39082.67932.86091.06857.9313-0.0197-0.52780.1464-0.39860.2625-0.7581-0.97260.69410.07851.00540.07920.03891.13780.11351.18914.2675-6.0037286.7148
716.41053.83032.54488.43542.47111.2507-0.11051.149-0.4711-0.31960.040.98980.1223-0.1366-0.03120.86110.0753-0.11481.0860.26621.042116.9273-14.3632283.1126
722.9774-0.14751.54482.1505-0.04443.95620.0838-0.3293-0.47030.16780.0670.38320.0873-0.05790.00060.85780.05390.18871.08320.38031.230910.0815-15.3571292.6525
734.831.26394.16951.8211.79634.18130.1478-1.5947-0.82330.1623-0.3375-0.1079-0.38810.01280.04531.2559-0.00840.24831.59060.40620.98624.5634-8.9416311.1028
741.5409-0.95480.63772.1480.78271.1112-0.9262-0.16850.72720.3354-0.3125-1.17070.2105-0.82030.10631.85760.20620.03841.8781-0.06741.083717.8236-10.9794332.355
750.74440.03620.68493.2823-0.71460.9704-0.1034-0.2149-0.52661.25180.3983-1.46910.071-1.30110.05261.88340.05370.21861.40150.05241.395623.8408-19.6988321.4547
762.62090.83150.37167.7237-1.5882.851-0.11330.2868-0.0419-0.26450.9486-0.0162-0.1391-0.354-0.20831.15320.21410.13721.4596-0.02321.07217.3405-8.4863318.3865
773.62640.32372.30644.0797-0.84684.44020.286-1.1067-1.70740.7577-0.4224-0.15850.4577-0.9186-0.30191.39010.0778-0.17451.68330.22061.54819.5923-16.1682328.7935
788.1208-1.5557-5.48330.6449-0.23218.88310.91460.75610.6914-0.60020.9305-1.19760.06610.6307-1.41131.93070.1049-0.13612.14190.1231.827229.8644-15.3381327.7499
791.40711.22091.20211.319-0.48463.81520.1947-0.6752-0.82610.4155-0.05670.38010.1029-0.5797-0.1121.1548-0.11830.07051.68350.59851.6294-7.8732-21.7286300.6135
801.52770.5684-0.34034.4338-0.27712.3518-0.2367-0.56670.44820.97321.14760.9959-0.0059-0.7323-0.47841.61670.15750.22371.48020.15331.03349.9733-9.1006326.04
814.04682.46390.1252.4217-1.49631.7045-0.0564-0.9260.27140.60350.13471.0030.0179-1.0732-0.35011.47080.11310.38431.77660.37451.08942.6457-11.962324.5709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 153 )
5X-RAY DIFFRACTION5chain 'A' and (resid 154 through 180 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 18 )
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 77 )
9X-RAY DIFFRACTION9chain 'B' and (resid 78 through 97 )
10X-RAY DIFFRACTION10chain 'B' and (resid 98 through 122 )
11X-RAY DIFFRACTION11chain 'B' and (resid 123 through 154 )
12X-RAY DIFFRACTION12chain 'B' and (resid 155 through 177 )
13X-RAY DIFFRACTION13chain 'B' and (resid 178 through 189 )
14X-RAY DIFFRACTION14chain 'C' and (resid -3 through 11 )
15X-RAY DIFFRACTION15chain 'D' and (resid 0 through 101 )
16X-RAY DIFFRACTION16chain 'D' and (resid 102 through 115 )
17X-RAY DIFFRACTION17chain 'D' and (resid 116 through 198 )
18X-RAY DIFFRACTION18chain 'E' and (resid 0 through 123 )
19X-RAY DIFFRACTION19chain 'E' and (resid 124 through 244 )
20X-RAY DIFFRACTION20chain 'F' and (resid 1 through 76 )
21X-RAY DIFFRACTION21chain 'F' and (resid 77 through 87 )
22X-RAY DIFFRACTION22chain 'F' and (resid 88 through 180 )
23X-RAY DIFFRACTION23chain 'G' and (resid 3 through 18 )
24X-RAY DIFFRACTION24chain 'G' and (resid 19 through 32 )
25X-RAY DIFFRACTION25chain 'G' and (resid 33 through 64 )
26X-RAY DIFFRACTION26chain 'G' and (resid 65 through 77 )
27X-RAY DIFFRACTION27chain 'G' and (resid 78 through 132 )
28X-RAY DIFFRACTION28chain 'G' and (resid 133 through 189 )
29X-RAY DIFFRACTION29chain 'H' and (resid -3 through 11 )
30X-RAY DIFFRACTION30chain 'I' and (resid 0 through 115 )
31X-RAY DIFFRACTION31chain 'I' and (resid 116 through 198 )
32X-RAY DIFFRACTION32chain 'J' and (resid 0 through 123 )
33X-RAY DIFFRACTION33chain 'J' and (resid 124 through 244 )
34X-RAY DIFFRACTION34chain 'K' and (resid 1 through 55 )
35X-RAY DIFFRACTION35chain 'K' and (resid 56 through 87 )
36X-RAY DIFFRACTION36chain 'K' and (resid 88 through 153 )
37X-RAY DIFFRACTION37chain 'K' and (resid 154 through 180 )
38X-RAY DIFFRACTION38chain 'L' and (resid 3 through 18 )
39X-RAY DIFFRACTION39chain 'L' and (resid 19 through 51 )
40X-RAY DIFFRACTION40chain 'L' and (resid 52 through 64 )
41X-RAY DIFFRACTION41chain 'L' and (resid 65 through 77 )
42X-RAY DIFFRACTION42chain 'L' and (resid 78 through 88 )
43X-RAY DIFFRACTION43chain 'L' and (resid 89 through 122 )
44X-RAY DIFFRACTION44chain 'L' and (resid 123 through 132 )
45X-RAY DIFFRACTION45chain 'L' and (resid 133 through 144 )
46X-RAY DIFFRACTION46chain 'L' and (resid 145 through 177 )
47X-RAY DIFFRACTION47chain 'L' and (resid 178 through 189 )
48X-RAY DIFFRACTION48chain 'M' and (resid -3 through 10 )
49X-RAY DIFFRACTION49chain 'N' and (resid 0 through 101 )
50X-RAY DIFFRACTION50chain 'N' and (resid 102 through 134 )
51X-RAY DIFFRACTION51chain 'N' and (resid 135 through 198 )
52X-RAY DIFFRACTION52chain 'O' and (resid 3 through 123 )
53X-RAY DIFFRACTION53chain 'O' and (resid 124 through 244 )
54X-RAY DIFFRACTION54chain 'P' and (resid 2 through 14 )
55X-RAY DIFFRACTION55chain 'P' and (resid 15 through 26 )
56X-RAY DIFFRACTION56chain 'P' and (resid 27 through 76 )
57X-RAY DIFFRACTION57chain 'P' and (resid 77 through 87 )
58X-RAY DIFFRACTION58chain 'P' and (resid 88 through 102 )
59X-RAY DIFFRACTION59chain 'P' and (resid 103 through 123 )
60X-RAY DIFFRACTION60chain 'P' and (resid 124 through 134 )
61X-RAY DIFFRACTION61chain 'P' and (resid 135 through 166 )
62X-RAY DIFFRACTION62chain 'P' and (resid 167 through 180 )
63X-RAY DIFFRACTION63chain 'Q' and (resid 3 through 32 )
64X-RAY DIFFRACTION64chain 'Q' and (resid 33 through 64 )
65X-RAY DIFFRACTION65chain 'Q' and (resid 65 through 132 )
66X-RAY DIFFRACTION66chain 'Q' and (resid 133 through 189 )
67X-RAY DIFFRACTION67chain 'R' and (resid -3 through 10 )
68X-RAY DIFFRACTION68chain 'S' and (resid 0 through 36 )
69X-RAY DIFFRACTION69chain 'S' and (resid 37 through 48 )
70X-RAY DIFFRACTION70chain 'S' and (resid 49 through 63 )
71X-RAY DIFFRACTION71chain 'S' and (resid 64 through 73 )
72X-RAY DIFFRACTION72chain 'S' and (resid 74 through 101 )
73X-RAY DIFFRACTION73chain 'S' and (resid 102 through 115 )
74X-RAY DIFFRACTION74chain 'S' and (resid 116 through 134 )
75X-RAY DIFFRACTION75chain 'S' and (resid 135 through 149 )
76X-RAY DIFFRACTION76chain 'S' and (resid 150 through 164 )
77X-RAY DIFFRACTION77chain 'S' and (resid 165 through 183 )
78X-RAY DIFFRACTION78chain 'S' and (resid 184 through 198 )
79X-RAY DIFFRACTION79chain 'T' and (resid 3 through 123 )
80X-RAY DIFFRACTION80chain 'T' and (resid 124 through 161 )
81X-RAY DIFFRACTION81chain 'T' and (resid 162 through 244 )

+
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