[English] 日本語
Yorodumi
- PDB-4p2r: Crystal structure of the 5cc7 TCR in complex with 5c1/I-Ek -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p2r
TitleCrystal structure of the 5cc7 TCR in complex with 5c1/I-Ek
Components
  • (5cc7 T-cell receptor ...) x 2
  • 5c1 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


peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosomal 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / 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 / Resolution: 3.295 Å
AuthorsBirnbaum, M.E. / Ozkan, E. / Garcia, K.C.
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 27, 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_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 1.6Jul 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 1.7Dec 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 1.8Nov 20, 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: 5c1 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: 5c1 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: 5c1 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: 5c1 peptide
S: 5cc7 T-cell receptor alpha chain
T: 5cc7 T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,34825
Polymers407,24220
Non-polymers1,1065
Water00
1
A: H-2 class II histocompatibility antigen, E-K alpha chain
B: MHC class II E-beta-k
C: 5c1 peptide
D: 5cc7 T-cell receptor alpha chain
E: 5cc7 T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2537
Polymers101,8105
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: 5c1 peptide
I: 5cc7 T-cell receptor alpha chain
J: 5cc7 T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0326
Polymers101,8105
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: 5c1 peptide
N: 5cc7 T-cell receptor alpha chain
O: 5cc7 T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2537
Polymers101,8105
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: 5c1 peptide
S: 5cc7 T-cell receptor alpha chain
T: 5cc7 T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)101,8105
Polymers101,8105
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)261.601, 101.867, 214.642
Angle α, β, γ (deg.)90.00, 94.89, 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 BL21 (bacteria) / Strain (production host): BL21
#5: Protein
5cc7 T-cell receptor beta chain


Mass: 29610.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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

#3: Protein/peptide
5c1 peptide


Mass: 1383.612 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: 3.47 Å3/Da / Density % sol: 64.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M Potassium citrate, 18% PEG 3350, 4% 1,3 butanediol

-
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 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.29→39.81 Å / Num. obs: 84239 / % possible obs: 98.8 % / Redundancy: 6.8 % / Rsym value: 0.143 / Net I/σ(I): 10.9
Reflection shellResolution: 3.29→3.36 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.356 / Mean I/σ(I) obs: 1.3 / % possible all: 84.9

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 3.295→39.454 Å / SU ML: 0.38 / σ(F): 1.33 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 4213 5 %
Rwork0.2117 --
obs0.2133 84239 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.295→39.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25581 0 70 0 25651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726332
X-RAY DIFFRACTIONf_angle_d0.81635764
X-RAY DIFFRACTIONf_dihedral_angle_d12.8999414
X-RAY DIFFRACTIONf_chiral_restr0.0383889
X-RAY DIFFRACTIONf_plane_restr0.0044715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.295-3.33230.41251050.35621967X-RAY DIFFRACTION74
3.3323-3.37150.39171390.31862686X-RAY DIFFRACTION100
3.3715-3.41260.30851330.30882719X-RAY DIFFRACTION100
3.4126-3.45570.31481280.31112646X-RAY DIFFRACTION99
3.4557-3.50120.29491570.28822683X-RAY DIFFRACTION99
3.5012-3.54910.29011310.27732645X-RAY DIFFRACTION99
3.5491-3.59980.30331430.27212673X-RAY DIFFRACTION98
3.5998-3.65350.30871100.26382716X-RAY DIFFRACTION100
3.6535-3.71050.28751170.26692692X-RAY DIFFRACTION100
3.7105-3.77130.29651400.25942725X-RAY DIFFRACTION100
3.7713-3.83630.28751450.25712665X-RAY DIFFRACTION100
3.8363-3.9060.28711520.24512694X-RAY DIFFRACTION100
3.906-3.9810.27011490.23442643X-RAY DIFFRACTION100
3.981-4.06220.24351390.22662676X-RAY DIFFRACTION100
4.0622-4.15040.26231520.22912689X-RAY DIFFRACTION100
4.1504-4.24690.25141490.21222727X-RAY DIFFRACTION100
4.2469-4.3530.23211330.19642656X-RAY DIFFRACTION99
4.353-4.47050.20151660.1822655X-RAY DIFFRACTION99
4.4705-4.60190.17341090.17122700X-RAY DIFFRACTION100
4.6019-4.75020.20751570.17062696X-RAY DIFFRACTION100
4.7502-4.91960.20951440.17282689X-RAY DIFFRACTION100
4.9196-5.11620.18071180.17712743X-RAY DIFFRACTION100
5.1162-5.34850.21881630.18452666X-RAY DIFFRACTION100
5.3485-5.62980.23951550.19292705X-RAY DIFFRACTION99
5.6298-5.98130.2571520.21582652X-RAY DIFFRACTION99
5.9813-6.44130.24111410.21732715X-RAY DIFFRACTION100
6.4413-7.08620.24351490.20212711X-RAY DIFFRACTION100
7.0862-8.10380.21551540.18412716X-RAY DIFFRACTION99
8.1038-10.18090.2261390.16932723X-RAY DIFFRACTION98
10.1809-39.45710.23771440.21032753X-RAY DIFFRACTION97
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.2965.23340.50086.9043-0.95042.906-0.0699-0.3326-0.9252-0.2507-0.17060.19160.11950.32510.28830.82360.19430.04910.65710.02750.8283-51.4083-15.255442.4402
27.75023.9730.7356.0518-0.05752.9443-0.24820.9573-0.5796-0.93150.2513-0.4309-0.13130.01310.02890.73580.15790.09650.7356-0.02580.7698-49.7862-14.502434.7565
34.7884-1.83020.45874.45980.82891.5683-0.2357-0.2555-0.7908-0.08060.2394-0.17030.21170.3245-0.080.74160.1590.17420.73020.09781.1183-40.2153-27.446647.1366
46.29582.61740.86174.92861.90014.70480.0528-0.583-1.53370.9991-0.0416-1.61160.72590.263-0.12330.87150.30590.11340.92140.13691.4502-33.2305-34.53650.8628
52.54135.98270.47737.90430.83552.82990.588-0.57720.01920.5433-0.32250.4329-0.14450.1934-0.28380.81990.1008-0.02720.57070.08990.7484-53.2074-9.504147.7278
66.5311-6.05391.40728.3666-0.99413.3769-0.2951-0.47490.85630.7526-0.0002-0.2983-0.69430.09790.23130.94040.02820.03290.6848-0.02090.7023-52.88332.210749.8532
73.42470.5692-0.63374.26360.18741.7566-0.0362-0.1774-0.8592-0.17180.11241.20910.3196-0.1946-0.11240.76350.06130.03440.61740.07081.1004-62.291-22.777944.8404
85.82321.55993.55646.6785-1.21137.44420.7204-1.6578-0.24991.3304-0.38341.05490.9659-0.7982-0.4151.3146-0.06760.26951.08360.21151.4113-59.7055-39.951658.3385
93.60114.5053-0.42496.9843-1.18874.2385-0.10050.61090.3896-0.6896-0.09620.23240.0337-0.1820.07610.72080.09450.10940.71060.02840.8525-55.7237-6.417535.2222
107.0367-2.62742.72816.2137-4.32774.68670.09590.44150.2329-0.11740.05550.0834-0.26-0.2999-0.1680.92560.18150.06250.91960.00930.7622-75.85247.406524.1951
114.90991.807-1.28983.4943-0.57655.3507-0.10991.41590.1859-0.55070.04440.5654-0.2573-0.91730.0971.45510.43260.03011.86920.30871.6483-85.419728.71740.5337
124.4294-0.33390.84283.9546-4.25487.7080.17130.9247-0.1082-0.3369-0.1983-0.4311-0.06580.4849-0.01441.02750.23250.18141.0680.03930.9034-53.358410.654415.0259
136.8847-0.7993-2.43654.32010.04794.52210.42270.76110.8002-0.0699-0.03270.5249-0.54050.0329-0.42131.39920.31460.17991.58130.52841.0448-69.602432.99154.3651
149.1363-5.61740.82587.3064-2.04542.462-0.0326-1.06120.43820.74060.1479-0.3711-0.33280.2846-0.15181.1604-0.03430.0990.92-0.04590.7976-49.8426-0.670778.7177
153.1533.5752-1.41893.9065-1.9232.02240.3114-0.65210.61080.3034-0.0056-0.969-0.66220.7165-0.22481.1951-0.2419-0.13291.2337-0.14581.1231-37.145712.82770.4292
164.52810.26330.12454.1742-0.01954.36530.4117-0.87460.95840.18790.1857-1.1661-0.99770.8278-0.48751.474-0.30760.17811.2712-0.26251.4617-35.610716.263275.1205
173.9115-5.21274.01277.9634-2.56957.48720.57030.0312-0.18490.7483-0.28620.0123-0.45271.0108-0.22570.891-0.03230.05730.94120.01390.795-44.1648-4.213970.271
188.6758-3.27233.3173.9012-0.42754.84630.68381.08390.4083-0.152-0.69340.3280.00280.4517-0.18340.8559-0.0120.09460.71320.0440.731-55.4368-5.462264.5713
195.23493.6608-0.48365.14413.57434.9385-0.12810.1009-0.95650.10290.2623-0.55630.06550.5936-0.10350.85230.14660.05750.7322-0.00590.8264-47.2272-16.086564.6079
209.75330.3080.50164.2101-0.43967.6957-0.2685-0.0799-0.8360.63080.89061.21980.001-0.8577-0.64650.85750.0710.00480.77180.12330.8684-61.033-16.057369.923
213.24250.6964-1.08973.8915-2.3931.10620.23970.17341.2133-0.00250.32820.7194-0.8391-0.2668-0.50021.53820.07270.23980.7853-0.07151.2797-58.614618.052965.6641
225.1047-0.5163-0.63927.1247-0.92712.36710.86210.81711.4321-1.7708-0.6398-0.0855-0.86460.1833-0.15851.93940.15940.4230.9460.04971.5188-53.912726.604258.4309
235.78613.88251.37174.0093-1.1263.0398-0.7016-0.9523-1.01671.85830.74130.3818-0.5125-0.4039-0.27721.11680.26550.05870.89690.00720.6423-55.1009-9.376578.3748
248.44943.9455-1.57425.3064-2.59263.77270.2876-0.3234-0.71770.0825-0.01870.13760.1878-0.2189-0.26241.01770.15070.04680.89530.18930.9604-76.6572-24.996381.1332
252.913-2.2460.03592.46920.6474.425-0.2272-0.5438-0.5850.08470.38510.85080.2398-1.2061-0.16991.718-0.257-0.10311.64160.4461.9258-92.2392-48.434898.9922
265.00110.7941-2.35572.751-1.29675.8002-0.0777-0.3616-0.734-0.0590.65710.08170.8488-0.2551-0.54451.40010.15940.04411.0830.28441.2101-56.9757-34.568995.6457
271.15181.7667-2.2035.6287-3.31174.83330.3489-0.54560.21060.9056-0.12840.0556-0.26370.6833-0.21941.24470.0293-0.01351.17440.21111.0825-58.2279-26.742196.8557
286.62821.61983.69923.54350.95226.12410.4618-0.1496-0.6191-0.09120.09020.41130.9277-0.0033-0.58961.7155-0.0602-0.02481.2570.3531.2197-75.8695-52.246100.1109
293.64760.28514.26224.6683-0.45617.8750.89-0.0615-1.1647-0.00870.0487-0.01730.5883-0.1878-0.73890.72090.23970.11911.16880.1610.9872-122.10345.677343.6962
305.50051.95495.26124.80764.3289.40210.9218-0.6225-1.2971-0.96310.6170.7203-0.9729-1.4971-1.31951.07270.4064-0.01011.14120.12071.2848-131.42349.526436.1774
311.88332.78370.73284.08222.10786.5347-0.2497-0.34710.8725-0.4607-0.03020.5504-0.0322-0.93570.35730.7930.3344-0.01771.16050.06931.3135-125.417717.28938.9588
329.69131.7911.39244.76684.39754.54740.36970.02440.9636-0.80260.2134-1.1321-1.62590.7509-0.27170.98170.0623-0.09270.91870.21771.3242-116.720120.697540.0033
337.42396.00162.10987.92613.644.0855-0.34430.7473-0.2094-1.5367-0.13541.53610.27550.15020.29261.00170.3348-0.1061.4723-0.12051.2462-131.03112.456926.5039
345.5005-0.4121-0.77545.38792.10634.23950.1282-0.6435-0.27740.2734-0.1036-0.51870.3172-0.4305-0.14650.79620.37350.131.22170.26011.3493-139.278112.305951.4362
352.6406-2.7293-3.39063.86265.66449.1421-0.1143-0.86170.1882-1.2460.9459-0.0401-0.87330.8797-0.8360.66510.2904-0.06131.2217-0.16131.1127-144.590815.597145.6822
368.1948-4.36620.37529.1399-0.94812.13350.90390.09660.7248-0.7744-0.72210.2491-0.18271.0624-0.14580.98890.0819-0.03931.27770.10211.2559-145.254526.173347.4944
375.181.78051.5837.65640.0624.0279-0.4599-1.56620.09530.09840.5954-0.3224-0.41540.3297-0.10690.76470.2592-0.03571.22120.05381.1274-137.534116.095650.7196
383.38131.4652.84595.60842.10132.78620.2599-1.1705-0.03461.1963-0.78550.70480.9251-0.54150.34810.95540.36930.16761.40220.20691.4947-148.29814.279952.339
399.03864.32626.2154.95682.68734.73730.0207-0.70810.213-0.12990.26140.67820.1719-0.3555-0.27690.7920.24350.07771.3233-0.02521.239-130.40220.863339.1108
402.17681.85621.013.28221.15942.4770.76780.2525-0.75560.1781-0.33340.15160.6008-0.0818-0.49610.94080.2775-0.11691.0268-0.05811.2554-122.1868-6.220640.1195
416.1034-1.2404-4.39915.376-1.57635.776-0.89761.6427-1.7075-1.9647-0.24130.2651.1075-0.91570.85110.90760.3306-0.191.6132-0.48451.6461-125.4082-12.480128.7072
422.96270.2299-0.01515.53352.63934.3345-0.0884-0.07710.8231-0.9433-0.1214-0.3136-0.34611.3280.17360.76360.276-0.03251.3289-0.35891.4135-111.9667-4.25631.7141
431.6604-2.6345-1.96797.84263.42974.8756-0.13720.69750.85190.43751.1542-0.4014-0.46681.5815-0.83260.70880.2351-0.03461.1824-0.01531.069-110.39859.421342.8513
445.10610.1372-1.34934.33910.70152.74530.6097-1.97930.71911.0631-0.0698-0.514-0.5041-0.8934-0.52331.15880.28470.02472.0984-0.21420.9637-123.745619.357664.0398
453.99835.10042.85696.86553.56292.0004-0.4069-1.8594-1.89573.8046-1.9064-1.37960.3226-1.82591.28941.56710.3318-0.0872.52030.35521.286-121.364712.274468.9764
469.05020.62350.87383.40581.81214.0944-0.3601-1.385-1.8564-1.79841.28770.1479-2.31730.9161-0.49382.9646-0.3373-0.21782.47180.07711.0531-127.31438.681779.6725
477.90482.3397-0.24397.6763.9258.80481.0975-1.75620.09851.6123-0.38650.94990.82630.3796-0.59761.21550.15440.13681.89030.03871.1711-127.244814.557566.4691
484.6912-1.5757-4.64997.60811.20934.57581.6379-2.3817-0.11070.5413-0.84140.3717-0.18312.221-0.52541.2745-0.04890.01352.7749-0.22421.2705-118.856820.405473.2972
492.37054.76315.5384.10594.0847.6254-0.6569-0.1074-0.2565-1.10710.00630.3958-0.8731-0.43440.6390.93450.4065-0.02551.27-0.14311.2711-119.45675.24430.6585
506.047-0.222-5.05692.25231.03245.6717-0.04720.6204-0.6109-0.2975-0.11330.2284-0.0991-0.2870.18570.91660.2703-0.09671.3363-0.06470.9371-96.02220.876918.5043
516.02480.17742.50157.526-4.44794.5948-0.75381.13170.4612-0.56280.0714-1.0657-0.4586-0.90810.74641.45830.1390.05091.9606-0.33171.3674-78.96720.988-9.9545
523.36331.6292-3.75992.786-2.54517.3142-0.12941.22910.2126-0.61880.32960.5089-0.1557-0.8896-0.17781.23070.3897-0.30032.1615-0.09821.2434-115.20557.39034.6162
534.677-1.8696-0.65045.1474-0.63041.3130.04481.5992-0.4053-0.6731-0.12210.5376-0.2094-0.97940.02671.50370.1283-0.17242.7037-0.41271.1254-94.8177-2.8515-14.1913
548.78615.3962-4.46684.8351-5.31767.34250.04381.217-1.8739-0.2118-0.1192-0.1652-0.1807-0.84060.01831.05820.0824-0.30470.9531-0.15181.6776-116.157-23.775148.855
552.0388-1.1522-6.85484.21711.5274.9173-0.52561.7361.47660.89591.2853-0.03241.594-1.2087-1.12741.20270.0482-0.39271.41750.10262.0012-125.5244-28.817351.9904
562.5459-0.3846-2.46365.33341.49768.6575-0.0895-0.067-1.07331.0758-0.18040.09810.66650.48130.40361.52430.1216-0.37931.0052-0.04752.1528-115.4888-36.8850.9369
578.9541-6.2654-0.58299.35321.10497.2296-0.0694-0.8301-0.43851.359-0.25550.99540.03640.29160.4311.0502-0.02460.02751.34340.36682.0603-128.6088-22.92561.9756
582.93660.51521.23910.035-0.1083.12510.1595-0.2876-0.1641-0.6804-0.74591.2660.3371-3.13540.81921.2897-0.0434-0.49131.784-0.05292.4473-138.3129-15.162247.692
597.02413.56821.99544.3955-2.22826.9328-1.4423-0.2393-1.5752-1.54221.15340.56231.0913-0.36070.48261.91610.0697-0.29341.5117-0.49452.0626-122.2141-38.674226.0356
600.6801-0.4291-0.40282.3138-0.1420.28180.17090.21271.0914-1.05230.0616-0.57440.4370.4014-0.58061.75960.2892-0.86681.6072-0.84512.3389-126.0891-31.743733.9757
612.9517-0.081-2.80438.3148-2.39373.10030.37171.37550.016-0.5064-0.1863-0.40242.4263-2.76070.11.6575-0.248-0.38631.7395-0.29291.9467-134.6992-34.215638.1278
624.8772.28046.44574.00552.21648.93280.9665-1.5807-1.8219-0.8504-1.72561.00740.3659-0.91790.3331.6294-0.0719-0.44661.638-0.25622.6301-133.9025-44.662535.3386
633.4119-0.04752.43144.10952.07858.33030.60390.9669-0.9077-0.5819-0.47090.78391.2939-0.5407-0.09191.52820.0779-0.54741.4269-0.37812.2871-128.0083-34.14834.8337
645.0164-5.0486-6.55638.0486.10588.62171.60142.2101-0.5849-0.5494-1.11990.76050.6537-2.4147-0.33381.5536-0.0693-0.48381.7509-0.18562.2719-136.5167-30.863930.372
655.2158-3.3131-3.1015.65141.9263.41280.51560.21320.4651-0.0488-0.16840.51680.0554-0.0173-0.28511.11760.1884-0.11521.02220.01071.31-119.0195-17.86150.4914
663.63433.57722.89325.08072.60276.0978-0.2214-0.6385-0.1611-0.21770.18920.8183-0.6787-0.84280.07660.99120.29380.04751.070.17181.4296-121.591-8.731757.7159
677.1148-2.7978-4.62514.67142.22816.65860.5472-0.8194-1.1947-0.0717-0.34750.4230.29470.3402-0.06530.9150.1123-0.08191.00510.05931.3676-109.3689-14.695463.4401
681.7895-0.3016-0.2121.13381.54324.44240.46811.0898-0.8905-0.88370.35490.01950.47661.375-0.79221.79120.4807-0.37511.6018-0.46241.993-106.6933-30.680932.8373
690.6314-0.83810.50411.04651.61994.35990.65830.32640.2863-0.48660.4214-0.58210.11931.228-1.0921.76820.4143-0.04781.8851-0.27951.7618-108.6513-29.341820.8481
705.7493-5.3739-4.8455.18174.79874.5746-2.0561-1.637-2.68071.48521.83641.31711.5021-0.00590.04581.04890.1460.04871.22590.21751.8747-116.2454-24.739561.3487
713.36290.00452.71.62850.12895.85920.1813-0.5724-0.5885-0.0976-0.33420.59570.4176-0.32410.21561.02130.0943-0.00241.11560.31471.252-97.3757-23.717578.4909
722.6843-0.5239-2.4069.21960.6222.2957-0.0534-1.3118-0.44281.754-0.62820.2392-0.7007-0.77110.63431.1055-0.12580.10661.41470.24431.4614-105.7423-16.924684.5879
735.22071.21074.43627.75444.71287.26360.2711-0.4695-0.2291-0.5061.0692-1.3361-1.8688-0.4567-0.68281.06610.15140.09671.20540.26421.0859-97.8685-12.713473.824
746.4172.98713.10018.78274.1716.13550.28980.9269-0.6436-0.37330.29970.7163-0.15110.9509-0.5531.06280.1943-0.14391.11860.21581.1833-95.1624-21.143870.1944
754.93051.10463.67855.46892.714.4508-0.4952-0.0838-0.0162-0.03250.57131.0401-0.92860.1619-0.28590.99530.05870.261.36410.44341.4073-98.3945-17.776384.1848
767.41010.3663.69383.9438-0.58798.5320.4334-1.058-1.77690.05690.89931.0992-0.6677-1.541-1.12321.19510.05980.1431.07270.38891.6129-108.1399-29.133972.2177
772.30066.15236.82239.77657.06356.34340.5361-1.7533-0.7577-0.0067-0.6953-1.12390.1047-0.4866-0.10481.4490.2030.25831.81910.33121.1916-87.569-15.729198.1549
783.0302-3.67130.21976.29731.76171.9354-1.5938-1.38670.89091.32950.8135-0.17661.6284-0.13710.95011.91220.27930.062.0202-0.10561.3447-94.2346-17.8104119.38
798.75755.6331-4.08055.1503-6.19092.0723-0.98140.0668-2.29261.14740.4209-2.76260.2797-1.57340.591.9796-0.01730.36061.7076-0.02051.8389-88.2843-26.4811108.4479
805.32144.6708-4.13194.6525-3.73936.89110.1268-0.861-0.82161.02790.1397-0.1321-0.1208-0.1427-0.12231.41180.1011-0.07951.74010.04221.4658-93.5449-19.3892110.9492
812.437-1.97891.59641.8992-0.87831.97340.38361.92520.87270.04530.807-0.9177-0.36790.2213-1.34882.231-0.1133-0.25262.27910.08951.9992-82.2461-22.1544114.7719
822.95750.20741.18223.7296-2.6918.94130.2036-0.6976-0.83190.3609-0.04850.6060.6057-0.9865-0.18231.2208-0.12290.11541.75210.49761.8264-120.4855-27.486185.2655
833.78652.67642.85798.75713.84794.07840.4827-1.0408-0.34811.73260.58860.62670.5846-0.9522-1.04361.94970.12180.27281.85230.40561.2127-106.1924-20.9936110.8736
845.64832.98030.374.8261-1.29552.69290.0303-0.9519-0.13710.64050.14270.75560.0813-1.3362-0.17181.75420.18950.43352.14620.33271.3101-109.4435-18.6395111.6587
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 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 153 )
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 180 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 32 )
6X-RAY DIFFRACTION6chain 'B' and (resid 33 through 64 )
7X-RAY DIFFRACTION7chain 'B' and (resid 65 through 122 )
8X-RAY DIFFRACTION8chain 'B' and (resid 123 through 189 )
9X-RAY DIFFRACTION9chain 'C' and (resid -3 through 10 )
10X-RAY DIFFRACTION10chain 'D' and (resid 0 through 115 )
11X-RAY DIFFRACTION11chain 'D' and (resid 116 through 198 )
12X-RAY DIFFRACTION12chain 'E' and (resid 0 through 123 )
13X-RAY DIFFRACTION13chain 'E' and (resid 124 through 244 )
14X-RAY DIFFRACTION14chain 'F' and (resid 1 through 76 )
15X-RAY DIFFRACTION15chain 'F' and (resid 77 through 102 )
16X-RAY DIFFRACTION16chain 'F' and (resid 103 through 180 )
17X-RAY DIFFRACTION17chain 'G' and (resid 3 through 18 )
18X-RAY DIFFRACTION18chain 'G' and (resid 19 through 32 )
19X-RAY DIFFRACTION19chain 'G' and (resid 33 through 64 )
20X-RAY DIFFRACTION20chain 'G' and (resid 65 through 77 )
21X-RAY DIFFRACTION21chain 'G' and (resid 78 through 132 )
22X-RAY DIFFRACTION22chain 'G' and (resid 133 through 189 )
23X-RAY DIFFRACTION23chain 'H' and (resid -3 through 10 )
24X-RAY DIFFRACTION24chain 'I' and (resid 0 through 115 )
25X-RAY DIFFRACTION25chain 'I' and (resid 116 through 198 )
26X-RAY DIFFRACTION26chain 'J' and (resid 0 through 30 )
27X-RAY DIFFRACTION27chain 'J' and (resid 31 through 123 )
28X-RAY DIFFRACTION28chain 'J' and (resid 124 through 244 )
29X-RAY DIFFRACTION29chain 'K' and (resid 1 through 14 )
30X-RAY DIFFRACTION30chain 'K' and (resid 15 through 26 )
31X-RAY DIFFRACTION31chain 'K' and (resid 27 through 45 )
32X-RAY DIFFRACTION32chain 'K' and (resid 46 through 55 )
33X-RAY DIFFRACTION33chain 'K' and (resid 56 through 76 )
34X-RAY DIFFRACTION34chain 'K' and (resid 77 through 112 )
35X-RAY DIFFRACTION35chain 'K' and (resid 113 through 123 )
36X-RAY DIFFRACTION36chain 'K' and (resid 124 through 134 )
37X-RAY DIFFRACTION37chain 'K' and (resid 135 through 160 )
38X-RAY DIFFRACTION38chain 'K' and (resid 161 through 180 )
39X-RAY DIFFRACTION39chain 'L' and (resid 3 through 18 )
40X-RAY DIFFRACTION40chain 'L' and (resid 19 through 51 )
41X-RAY DIFFRACTION41chain 'L' and (resid 52 through 64 )
42X-RAY DIFFRACTION42chain 'L' and (resid 65 through 77 )
43X-RAY DIFFRACTION43chain 'L' and (resid 78 through 88 )
44X-RAY DIFFRACTION44chain 'L' and (resid 89 through 122 )
45X-RAY DIFFRACTION45chain 'L' and (resid 123 through 132 )
46X-RAY DIFFRACTION46chain 'L' and (resid 133 through 144 )
47X-RAY DIFFRACTION47chain 'L' and (resid 145 through 177 )
48X-RAY DIFFRACTION48chain 'L' and (resid 178 through 189 )
49X-RAY DIFFRACTION49chain 'M' and (resid -3 through 10 )
50X-RAY DIFFRACTION50chain 'N' and (resid 0 through 115 )
51X-RAY DIFFRACTION51chain 'N' and (resid 116 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 55 )
57X-RAY DIFFRACTION57chain 'P' and (resid 56 through 76 )
58X-RAY DIFFRACTION58chain 'P' and (resid 77 through 87 )
59X-RAY DIFFRACTION59chain 'P' and (resid 88 through 102 )
60X-RAY DIFFRACTION60chain 'P' and (resid 103 through 112 )
61X-RAY DIFFRACTION61chain 'P' and (resid 113 through 123 )
62X-RAY DIFFRACTION62chain 'P' and (resid 124 through 134 )
63X-RAY DIFFRACTION63chain 'P' and (resid 135 through 166 )
64X-RAY DIFFRACTION64chain 'P' and (resid 167 through 180 )
65X-RAY DIFFRACTION65chain 'Q' and (resid 3 through 32 )
66X-RAY DIFFRACTION66chain 'Q' and (resid 33 through 64 )
67X-RAY DIFFRACTION67chain 'Q' and (resid 65 through 77 )
68X-RAY DIFFRACTION68chain 'Q' and (resid 78 through 132 )
69X-RAY DIFFRACTION69chain 'Q' and (resid 133 through 189 )
70X-RAY DIFFRACTION70chain 'R' and (resid -3 through 10 )
71X-RAY DIFFRACTION71chain 'S' and (resid 0 through 36 )
72X-RAY DIFFRACTION72chain 'S' and (resid 37 through 48 )
73X-RAY DIFFRACTION73chain 'S' and (resid 49 through 63 )
74X-RAY DIFFRACTION74chain 'S' and (resid 64 through 73 )
75X-RAY DIFFRACTION75chain 'S' and (resid 74 through 90 )
76X-RAY DIFFRACTION76chain 'S' and (resid 91 through 101 )
77X-RAY DIFFRACTION77chain 'S' and (resid 102 through 115 )
78X-RAY DIFFRACTION78chain 'S' and (resid 116 through 134 )
79X-RAY DIFFRACTION79chain 'S' and (resid 135 through 149 )
80X-RAY DIFFRACTION80chain 'S' and (resid 150 through 183 )
81X-RAY DIFFRACTION81chain 'S' and (resid 184 through 198 )
82X-RAY DIFFRACTION82chain 'T' and (resid 3 through 108 )
83X-RAY DIFFRACTION83chain 'T' and (resid 109 through 161 )
84X-RAY DIFFRACTION84chain '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