[English] 日本語
Yorodumi
- PDB-7n6e: TCR peptide HLA-A2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n6e
TitleTCR peptide HLA-A2 complex
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Spike protein S1
  • TRAV12-1 TCR-alpha
  • TRBV19 TCR beta
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / T cell receptor / Human Leucocyte Antigen / SARS-CoV-2 / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane ...antigen processing and presentation of peptide antigen via MHC class I / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / amyloid fibril formation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / intracellular iron ion homeostasis / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / learning or memory / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / immune response / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Spike glycoprotein / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsChaurasia, P. / Rossjohn, J. / Petersen, J.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein.
Authors: Chaurasia, P. / Nguyen, T.H.O. / Rowntree, L.C. / Juno, J.A. / Wheatley, A.K. / Kent, S.J. / Kedzierska, K. / Rossjohn, J. / Petersen, J.
History
DepositionJun 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / refine_hist
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high
Revision 1.2Sep 22, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
D: MHC class I antigen
E: Beta-2-microglobulin
F: Spike protein S1
G: TRAV12-1 TCR-alpha
I: TRAV12-1 TCR-alpha
H: TRBV19 TCR beta
J: TRBV19 TCR beta


Theoretical massNumber of molelcules
Total (without water)190,55310
Polymers190,55310
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S1
I: TRAV12-1 TCR-alpha
J: TRBV19 TCR beta


Theoretical massNumber of molelcules
Total (without water)95,2775
Polymers95,2775
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: Spike protein S1
G: TRAV12-1 TCR-alpha
H: TRBV19 TCR beta


Theoretical massNumber of molelcules
Total (without water)95,2775
Polymers95,2775
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.832, 95.131, 168.755
Angle α, β, γ (deg.)90.000, 100.182, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 20 or resid 23...
d_2ens_1(chain "D" and (resid 1 through 16 or (resid 17...
d_1ens_2(chain "B" and (resid 1 through 37 or (resid 38...
d_2ens_2(chain "E" and (resid 1 through 57 or (resid 58...
d_1ens_3chain "C"
d_2ens_3chain "F"
d_1ens_4(chain "G" and (resid 1 through 2 or resid 4...
d_2ens_4(chain "I" and ((resid 1 through 2 and (name N...
d_1ens_5(chain "H" and (resid 3 through 13 or (resid 14...
d_2ens_5(chain "J" and (resid 3 through 14 or resid 16...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYPROA1 - 20
d_12ens_1ILEGLYA23 - 175
d_13ens_1GLUGLUA177 - 251
d_14ens_1ARGTRPA253 - 271
d_21ens_1GLYPROD1 - 20
d_22ens_1ILEGLYD23 - 175
d_23ens_1GLUGLUD177 - 222
d_24ens_1GLNGLUD226 - 254
d_25ens_1ARGTRPD256 - 274
d_11ens_2ILETHRB1 - 68
d_12ens_2PHEMETB70 - 99
d_21ens_2ILETHRE1 - 68
d_22ens_2PHEMETE70 - 99
d_11ens_3TYRLEUC1 - 9
d_21ens_3TYRLEUF1 - 9
d_11ens_4ARGLYSG1 - 2
d_12ens_4VALASNG4 - 91
d_13ens_4ASNLEUG93 - 120
d_14ens_4ASPSERG122 - 138
d_15ens_4THRASNG140 - 175
d_16ens_4SERALAG177 - 180
d_17ens_4ALASERG182 - 198
d_21ens_4ARGLYSH1 - 2
d_22ens_4VALASNH4 - 91
d_23ens_4ASNLEUH93 - 120
d_24ens_4ASPSERH122 - 138
d_25ens_4THRASNH140 - 175
d_26ens_4SERALAH177 - 180
d_27ens_4ALASERH182 - 198
d_11ens_5GLYLYSI1 - 12
d_12ens_5GLYALAI14 - 59
d_13ens_5GLYLEUI61 - 110
d_14ens_5ASPSERI112 - 127
d_15ens_5ALAALAI129 - 239
d_21ens_5GLYLYSJ1 - 12
d_22ens_5GLYALAJ14 - 59
d_23ens_5GLYLEUJ61 - 110
d_24ens_5ASPSERJ112 - 127
d_25ens_5ALAALAJ129 - 239

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

-
Components

#1: Protein MHC class I antigen / HLA-A*02:01


Mass: 32125.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q861F7
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Spike protein S1


Mass: 1151.377 Da / Num. of mol.: 2 / Fragment: epitope YLQPRTFLL (UNP residues 269-277) / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#4: Protein TRAV12-1 TCR-alpha


Mass: 22680.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein TRBV19 TCR beta


Mass: 27440.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.2 M sodium thiocyanate, 100 mM Tris-Cl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 3.2→47.85 Å / Num. obs: 31387 / % possible obs: 95.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 53.86 Å2 / CC1/2: 0.842 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.168 / Rrim(I) all: 0.259 / Net I/σ(I): 4.16
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3149 / CC1/2: 0.381 / Rpim(I) all: 0.628 / Rrim(I) all: 0.889 / % possible all: 96.17

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 6VRM & 3GSO

6vrm

3gso


Resolution: 3.2→47.85 Å / SU ML: 0.4991 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0272
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2941 1994 6.36 %
Rwork0.2389 29365 -
obs0.2424 31359 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.92 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12993 0 0 0 12993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001713336
X-RAY DIFFRACTIONf_angle_d0.480418135
X-RAY DIFFRACTIONf_chiral_restr0.03931917
X-RAY DIFFRACTIONf_plane_restr0.00342385
X-RAY DIFFRACTIONf_dihedral_angle_d12.35154779
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.839363330303
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.62747239221
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.256578909776
ens_4d_2GX-RAY DIFFRACTIONTorsion NCS0.898639464388
ens_5d_2IX-RAY DIFFRACTIONTorsion NCS0.760528897261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.38191450.31812110X-RAY DIFFRACTION96.29
3.28-3.370.35291410.30072126X-RAY DIFFRACTION95.53
3.37-3.470.35481460.30352100X-RAY DIFFRACTION96.6
3.47-3.580.34811500.27562098X-RAY DIFFRACTION95.78
3.58-3.710.3061370.26492104X-RAY DIFFRACTION96.14
3.71-3.860.30751420.252108X-RAY DIFFRACTION95.91
3.86-4.030.32931490.2462094X-RAY DIFFRACTION95.37
4.03-4.240.27081440.22952109X-RAY DIFFRACTION94.82
4.24-4.510.27151380.20522068X-RAY DIFFRACTION95.05
4.51-4.860.26891380.19632096X-RAY DIFFRACTION94.42
4.86-5.340.27381410.21252089X-RAY DIFFRACTION94.25
5.35-6.120.24331430.22652074X-RAY DIFFRACTION93.9
6.12-7.70.29951390.24252095X-RAY DIFFRACTION93.43
7.7-47.850.24591410.20722094X-RAY DIFFRACTION91.71
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)
13.470714500970.1161411482411.471941017482.253192787631.433493814232.910375062580.0565146635003-0.4008224497090.0460961087618-0.1571952076960.343689887088-0.04556237895620.01150056541610.523954977429-0.05073736576470.350338942531-0.1292618545560.1332648923150.41438592368-0.08597175224280.414743527108-4.99531675953-21.993777541853.2513847242
24.086104865240.9565841662742.434007210942.310338535591.149669535313.02500977830.758281483751-0.401061523474-0.826505164050.688249856803-0.221115740325-0.2271034534651.28927419462-0.133355066732-0.8535888139510.635352818881-0.0256500261893-0.2468232867080.4623269969860.1280278690080.84755598251919.9551292955-30.408979350976.1704637131
34.38115225245-0.127174766270.13014639313.01367372654-0.7627658710593.360941691010.001324168093750.0610360563633-0.00158231584682-0.143695640248-0.502707790852-1.094267966070.390519594130.632105350703-0.08963681446320.302705512442-0.173636978624-0.05525244292510.6685194602280.13818831630.6519448800818.8194934292-16.516059100568.4803161241
44.10081502929-0.792041923220.6228992167351.16219983785-0.6801367996531.233714979080.2153413824350.4673131671190.998723810073-0.156248947256-0.47465114207-1.17504257017-0.01680446586470.524754969910.2144948394270.3281701720880.07789925220810.02947832781550.3745653784320.2222955207121.0924158266216.2548149763-10.496121287964.5676507295
51.88742530081-0.311670282208-1.202776953861.82298078641-0.2506843389651.32084746728-0.1000887583240.6867126201390.916123523629-0.467881157373-0.344243502079-1.25297370969-0.2842260045020.5062660672520.3187695464030.9541966852120.2534312676120.3479823116070.5900534415360.4419672903311.4676698921419.696461917-7.8906866278457.5813378543
62.72160131931-1.096095461140.7729125462012.065756493710.7571845172122.647432518710.05660412319760.5343192606250.346491145778-0.143226617848-0.315896394969-0.330398941801-0.08935444047990.2992626211020.1283787284880.1918247595780.03217262247070.09246409179360.715446162920.1537564246980.6200208409811.548412569-15.988091970261.7918958084
74.46512668136-0.2995574289561.031034543150.2546085871240.1875628593792.98034752154-0.123057171528-0.09532564798421.39091713412-0.386058493967-0.233717302987-1.445410259530.03825789291060.3956196869470.2391813598570.5205638885030.0800705151246-0.09255436001940.4605608255610.01441852010221.2117049625121.4378957523-8.4837177151171.277578334
81.41418001235-0.413781238673-1.053711517420.9697491111140.2174341221442.020620941110.09502332161880.02329920607980.14621780836-0.100995946076-0.0167767649124-0.0862493664753-0.09752610021440.2834566655890.2918198235460.118248476634-0.02454308469980.07767458058070.4109879625090.2800520200840.272545443979-10.6367090773-23.223029987148.0635192088
93.34226235707-0.0603794879803-1.10150182261.97115105776-1.124657247611.956941618180.122612736720.0171976041403-0.6550279726510.2705380235960.210188028310.1756996597540.578288754346-0.5752064298730.02777836854070.435719905879-0.0971038811476-0.2834951891790.5190227695350.2296129515690.5776625433780.85710930669218.158461950651.7060977047
102.035302975180.508701990516-1.713434895580.5130580312-0.211399576861.573750376720.06792259485050.6621097991670.249694513006-0.3256399590710.1341508130820.3391165593570.048629058084-0.5175788610810.2849836827120.788869233419-0.111787578629-0.5045320357340.546548391360.1959258264471.11626149877-5.1165429844120.278160011341.7612007028
113.435766853690.343967969301-0.5438980241821.12871819514-1.173022755391.87107548182-0.0767213190935-0.490064603227-0.0967590756342-0.01536221997650.1756689285860.1533612780240.0321071288731-0.4746269887620.1438769231130.405493322992-0.108461564334-0.242189848660.373132381691-0.004766756430380.4669116549339.262783383719.809503167151.9643211693
123.70178199792.01910775575-0.5834453026523.20100537041-1.070923473082.096555963480.125015771138-0.7900640071620.1550308399390.533691406729-0.4953764135320.108014759379-0.583738565997-0.2069202641740.05749210596070.278003760799-0.169264140883-0.09806777337610.470187269064-0.08159701143180.2485332916115.682405307623.817005134363.0227324782
133.615853973240.759164843026-0.07339206859591.38736236665-0.2981724699271.175993551580.15423914028-0.1170982243370.4828981820080.0771879498762-0.1615857558560.051237582863-0.3113315559870.0256650959309-0.03048943022460.577715999981-0.11389608561-0.2139009639770.183341338932-0.068218819720.43620235846913.006284906829.777969273152.101276704
143.497493613010.685732363673-1.123146687221.05347829655-0.9183472700673.087991161480.782131641046-0.6341349701510.8294692247980.3003201216690.0922620888594-0.212508665226-0.742061253004-0.00476778338291-0.1595604627650.7190784299950.2421464335880.04409272894450.645010603669-0.466120590860.878563859465-17.347327386230.466842235774.4649826988
155.219926745580.22706410076-2.926972895661.64814688457-0.4810205566066.636969375090.247181119584-0.4461721980050.441461712716-0.0828236778660.2133662885520.348695382066-0.190986924017-0.286451532428-0.1377376458880.5193925321680.185823074305-0.2850684337330.546829823592-0.2242718729930.803128876945-16.236816403925.244490844771.3239733748
164.568877859690.894392769827-1.522785251651.96310549729-0.788724473581.437392017970.784453676135-0.93084253791.28010653839-0.01791081018210.2172159919340.225466466016-1.405942800690.229865791887-0.8095372042971.214558173440.1732450711110.1094047575990.81622575115-0.4343250088281.04043921553-19.691231331437.047473066579.4996278488
172.85806198363-3.76793909255-0.4372961170795.18093557460.05960201006771.38900766162-0.05382628776-0.219978720671-0.3875788606380.188644896244-0.0332445033790.3884310452670.01257900939930.2398085279790.06482829190080.124205702787-0.1726009328750.05965414527420.6435571339880.04133068043410.298531709459-3.5524748607212.570483747270.5277940088
183.797340525290.05381699403250.226061275220.0263623919187-0.2003926125671.87845031310.02674988287990.708987505227-0.866668205894-0.304614845012-0.5726703569781.16471719569-0.238881003843-0.61000701372-0.1357105438390.4542090504330.178685789476-0.1603260850930.526680258811-0.2836323286061.15762236789-18.074223573512.77103140563.1954356517
194.74466742918-1.74906307854-0.179305684670.939688823674-0.564314743631.705421059110.009417841168810.670896560795-0.3141054233-0.221847596321-0.3065108092910.696652369972-0.199086727093-0.5309245306860.04437029962690.4064647362090.338498134542-0.1580993402780.726605862062-0.1787755496870.478706008343-9.0534270987416.490125619860.9908313862
209.446828132492.727249830121.125317816893.94242636801-2.73079518775.871903081910.13646845744-0.368960135852-1.15793536356-0.2578121001660.1644920465531.0658129-0.0366978535845-1.27745715128-0.3104648730040.725187032020.25916353488-0.4626430056461.38630345425-0.09685248390682.07532485847-32.189531811410.653373950569.5933681461
212.43298442731-0.737652501780.897321576290.268178471917-0.620499696193.110416085880.117076061791-0.229662471703-1.30416756631-0.244308022757-0.06161086124291.093192248150.087473977142-0.3667029700710.02712199716570.322896787350.0817644471447-0.123084887590.478081487709-0.08740213724831.12197905731-11.28344451274.8877586171469.3503397914
224.87591930682-0.7938511911082.045296652450.5815639573060.06282649931822.9228148714-0.0073976436918-0.714519881199-0.403006798319-0.06684418098820.2711425042781.20991647857-0.481801847648-0.604149990125-0.03487117250490.7160503657680.1276199169540.2038757388450.6126162103860.3910015496161.26907336705-21.686163892613.401747081273.4927658933
232.142153081110.3317352972130.9489615668651.934897218391.237049640811.783681361540.0524189413508-0.375528382107-0.05276161064230.268711112416-0.0303496529746-0.1405795894550.139602367774-0.274475478028-0.2453232923380.385327227579-0.203445247049-0.1190156780340.313587129347-0.1016888940480.13709221921113.279482589223.504195609746.9548724887
241.739475179050.418018520022-0.3849499164940.592613860516-0.6440508415690.7474309526380.2956511797170.339413293828-0.00362848441058-0.2546019251960.01949672499340.09233829559650.165121188594-0.07989382332270.4265020336930.596681437185-0.128079562817-0.1434285009380.127358341830.1646005665640.15004280385128.77176083536.528774745432.9518912702
253.157784297740.7287951776110.2457346424610.520198995921-0.1443512000011.8076006124-0.0226382814284-0.5865326375820.05358825259630.389792714767-0.133707322526-0.118614854311-0.305724700795-0.228741191093-0.1574229855010.506194030572-0.0615485678007-0.1618122227750.2360089006340.06381797299650.21790048630128.990809067635.721317852239.2213290538
267.44969638121.45642235131-2.641036770812.33842993967-1.36503464891.67516423242-0.249388623226-0.1231292385370.1185087904610.272702638766-0.0669935982419-0.407326546911-0.265353661891-0.000442890031173-0.2026663198880.481236079703-0.00645093018405-0.105323806690.191210931489-0.06989790360460.081842560653949.312995034343.33353117626.5089278236
273.974541150450.482368173788-1.555125098021.99116601007-0.130079603712.79683417395-0.1467797270870.743415298455-0.389945758519-0.283031359522-0.0261256999883-0.016589083206-0.299125077561-0.439914505136-0.02483019237110.432803014255-0.191963289211-0.09116133083870.308143290160.09668895866990.44494723185255.389972412737.369446149813.0290120594
282.066150013550.423074774630.6061117634691.367857731120.1875547674860.7948910697370.209616682002-0.087403633050.08315045816030.102801615777-0.214689317754-0.01424156451320.2310745852830.0604616063734-0.1195675745310.528049875649-0.086001892099-0.09198724564090.157487516644-0.05013866958330.473605977786-26.0687562764-35.497375772537.1365592163
294.610600385351.485516643122.231697274321.054991434230.9770679073851.787018967330.233253372599-0.315497986407-0.167084476260.215492391982-0.1779734840350.09863875935260.516221603528-0.341777528073-0.4761892379980.620428607938-0.218839442744-0.1777338926320.1792285985520.0003061178913940.115833505167-46.2948988623-42.318934006326.7678398883
302.927461938740.5624916606920.05580786050311.653308202770.5677939036631.741319147590.1244560663540.2895878643290.192480591243-0.112658076278-0.1749728504040.0477400751840.0812875345385-0.133710082196-0.02029117485720.41216431388-0.101759374014-0.03285974253940.1328021037350.0544258105860.411573964428-52.7746664325-35.08899602413.4693042457
313.348229570850.154544439868-1.011039762682.751512761480.2836596487391.6029559931-0.4841554256230.181211506523-0.503031517324-0.1049958176710.221459908510.3847867714450.545203425777-0.1039668338850.1107769592830.466739921157-0.00208140672605-0.1082968742330.209985748528-0.01427413182950.56291696353225.11122678314.946514648828.3459331509
322.066513388610.260846225187-1.252661868391.612344125840.1202297751521.20051003058-0.1424160838480.410716769406-0.5275245283210.1308650904050.0362418144245-0.07519809488110.3377105355470.04380978064280.1065375903880.336374253540.0505794159746-0.01385110669510.293499322047-0.04763941722380.52017774626128.441689972414.765280962925.06585277
332.40799107430.658000580026-0.1615380109772.22521273935-0.03051563336831.01690321673-0.03495877400050.123619315978-0.3709959627770.0185427294545-0.164176032493-0.3653714376470.2057640813540.0212739109928-0.002511231906310.324468502927-0.03031037328950.03199412814460.193624500553-0.1079222871710.37038204150255.121474529124.754313625418.6166107185
341.0987975185-0.0461041108504-0.3926010284011.97058004310.0389647854582.01123586668-0.04815611614360.484483835016-0.847640686909-0.439119047686-0.194518062999-0.296838190140.384508743249-0.2242897485760.1448434045490.604854006347-0.07248104471220.06977343985050.318801909306-0.1487903649470.73015821561149.20859495459.5098451930412.4848521303
350.270556666508-0.42132667284-0.1402946677541.678986323320.9042698213370.5319307512370.03031003302990.04411480442110.374851107524-0.175176107007-0.16679176697-0.257897998451-0.659560718143-0.131843528247-0.2026291151170.6295652211690.0221007613657-0.1811152085480.0735528734843-0.1938085258220.998114913539-26.7307859104-12.267271371329.5846322934
361.659409251060.167223806434-0.2643435871581.60464664547-0.5701391224340.9584403580790.06801556032290.1539839662-0.0648944416266-0.201952655321-0.108899709243-0.538812531537-0.2396663985840.3352223093050.0370043551480.548002885364-0.1412339112540.08885824579820.216810434395-0.03979706092480.783199746666-15.6189108899-17.095894426530.5303191353
370.5377673852490.427938260596-0.1459377621961.78428480609-0.5380788928190.975402518941-0.425071680433-0.008633275904990.112585132801-0.1036381172440.0167532270032-0.182476141667-0.128414601625-0.03066016730180.1198399835330.806996155912-0.00944243084157-0.2508455873930.1505938082230.002318237294290.976615823986-20.269013921-10.041844360927.602616795
380.3828743831920.0001460733142710.04058294677010.6460054530560.02423192815670.8442025624180.0659455851007-0.131829415950.260349514230.37896528055-0.139341672030.00880869140902-0.272357106764-0.000949910892605-0.1044008810180.523771258878-0.1092842747790.06183447909360.0735081303496-0.1518305193040.632050706423-25.6900662341-19.734817558636.7816752259
390.1052530445970.105458179046-0.09787365901570.312866758726-0.05218336704280.0935012689743-0.04654764768340.01492187672530.188327537014-0.01338229369060.08684891206320.01163820171080.01168497368410.01016783424870.2375825399140.6462495293830.0342388000457-0.2125975451730.03622546356320.1194481877140.789781708096-33.972447449-12.451773381911.5987190865
401.804683706261.19736565251-0.4712701534883.027261658560.1483067483211.17031847146-0.04522144092240.1193086178340.2329091308930.03325193432660.02545068251630.7580573340150.154624713138-0.324526452617-0.4092371127290.440323839705-0.0849240405011-0.1389421546240.3157829092880.1724127894520.452473004521-58.2746307416-27.741196851917.4442111914
410.7550876542250.5766484952630.6562496104421.7094240193-0.7074300127641.71925273685-0.0780232273851-0.08847876727730.4316362140370.18549403836-0.3580327107560.371794462553-0.004909212652360.0425973971008-0.1254594179220.617387024978-0.0226279816493-0.03825292066820.131412328065-0.04320734104350.667535701654-48.7584214801-19.604382992625.3490562732
421.52983752727-0.762318726085-0.4222869587761.70961405883-0.8925076948615.5354361486-0.09742257977540.2037458014990.69002649228-0.316222266306-0.439121999692-0.386312641627-0.009735323360090.4734413930760.04814664582630.575178929599-0.03262182368590.05834344434020.2499473906020.09466686848520.649179448619-38.0442248744-23.866609242410.9244493659
430.3667330167160.2895828408270.2823619161410.3922575501920.3265051134440.2637448649570.111549557434-0.06292337509760.3329217008540.290290127083-0.2836304146240.585022688707-0.0269068266964-0.163072806275-0.4759965835360.857997951107-0.0151195698375-0.06259214013960.0606006610541-0.02639029022760.624652914168-57.3993781741-22.443126728723.1778236544
440.2777623261180.0570270200654-0.05375089505131.24098987773-0.1765489714330.491001498449-0.2960780000110.07862254609240.4091964964240.04420655143840.01601100582750.121692079547-0.0397926188409-0.0595475291509-0.3716395603840.76907991894-0.0605225096337-0.2368161460550.05467590387690.07178813062790.947321063482-46.3578487853-8.0527429519614.4610627603
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 174 )AA1 - 1741 - 174
22chain 'A' and (resid 175 through 274 )AA175 - 274175 - 271
33chain 'B' and (resid 1 through 19 )BB1 - 191 - 19
44chain 'B' and (resid 20 through 43 )BB20 - 4320 - 43
55chain 'B' and (resid 44 through 53 )BB44 - 5344 - 53
66chain 'B' and (resid 54 through 71 )BB54 - 7154 - 71
77chain 'B' and (resid 72 through 99 )BB72 - 9972 - 99
88chain 'C' and (resid 1 through 9 )CC1 - 91 - 9
99chain 'D' and (resid 1 through 37 )DD1 - 371 - 37
1010chain 'D' and (resid 38 through 56 )DD38 - 5638 - 56
1111chain 'D' and (resid 57 through 118 )DD57 - 11857 - 118
1212chain 'D' and (resid 119 through 137 )DD119 - 137119 - 137
1313chain 'D' and (resid 138 through 174 )DD138 - 174138 - 174
1414chain 'D' and (resid 175 through 230 )DD175 - 230175 - 230
1515chain 'D' and (resid 231 through 250 )DD231 - 250231 - 250
1616chain 'D' and (resid 251 through 274 )DD251 - 274251 - 274
1717chain 'E' and (resid 1 through 8 )EE1 - 81 - 8
1818chain 'E' and (resid 9 through 53 )EE9 - 539 - 53
1919chain 'E' and (resid 54 through 71 )EE54 - 7154 - 71
2020chain 'E' and (resid 72 through 77 )EE72 - 7772 - 77
2121chain 'E' and (resid 78 through 90 )EE78 - 9078 - 90
2222chain 'E' and (resid 91 through 99 )EE91 - 9991 - 99
2323chain 'F' and (resid 1 through 9 )FF1 - 91 - 9
2424chain 'G' and (resid 1 through 49 )GG1 - 491 - 43
2525chain 'G' and (resid 50 through 121 )GG50 - 12144 - 101
2626chain 'G' and (resid 122 through 135 )GG122 - 135102 - 115
2727chain 'G' and (resid 136 through 218 )GG136 - 218116 - 198
2828chain 'I' and (resid 1 through 121 )IH1 - 1211 - 101
2929chain 'I' and (resid 122 through 135 )IH122 - 135102 - 115
3030chain 'I' and (resid 136 through 219 )IH136 - 219116 - 199
3131chain 'H' and (resid 3 through 75 )HI3 - 751 - 61
3232chain 'H' and (resid 76 through 136 )HI76 - 13662 - 119
3333chain 'H' and (resid 137 through 227 )HI137 - 227120 - 210
3434chain 'H' and (resid 228 through 256 )HI228 - 256211 - 239
3535chain 'J' and (resid 3 through 44 )JJ3 - 441 - 35
3636chain 'J' and (resid 45 through 75 )JJ45 - 7536 - 61
3737chain 'J' and (resid 76 through 99 )JJ76 - 9962 - 84
3838chain 'J' and (resid 100 through 121 )JJ100 - 12185 - 104
3939chain 'J' and (resid 122 through 136 )JJ122 - 136105 - 119
4040chain 'J' and (resid 137 through 163 )JJ137 - 163120 - 146
4141chain 'J' and (resid 164 through 184 )JJ164 - 184147 - 167
4242chain 'J' and (resid 185 through 200 )JJ185 - 200168 - 183
4343chain 'J' and (resid 201 through 227 )JJ201 - 227184 - 210
4444chain 'J' and (resid 228 through 256 )JJ228 - 256211 - 239

+
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