[English] 日本語
Yorodumi
- PDB-8vcy: Human TCR A2.13 in complex with DQ8-InsC8-15NPY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vcy
TitleHuman TCR A2.13 in complex with DQ8-InsC8-15NPY
Components
  • (MHC class II HLA-DQ- ...) x 2
  • (T-CELL-RECEPTOR, TCR A2.13 ...) x 2
  • Hybrid insulin peptide (HIP; InsC8-15-NPY68-74)
KeywordsIMMUNE SYSTEM / Immune receptor complex
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane
Similarity search - Function
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 ...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 / Immunoglobulin-like fold
Similarity search - Domain/homology
PHOSPHATE ION / MHC class II HLA-DQ-beta-1 / MHC class II HLA-DQ-alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTran, T.M. / Lim, J.J. / Loh, T.Y. / Mannering, I.S. / Rossjohn, J. / Reid, H.H.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2008981 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1123586 Australia
CitationJournal: J.Biol.Chem. / Year: 2024
Title: A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8.
Authors: Tran, M.T. / Lim, J.J. / Loh, T.J. / Mannering, S.I. / Rossjohn, J. / Reid, H.H.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
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 / _citation_author.name
Revision 1.2Sep 4, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class II HLA-DQ-alpha chain
B: MHC class II HLA-DQ-beta-1
C: Hybrid insulin peptide (HIP; InsC8-15-NPY68-74)
D: T-CELL-RECEPTOR, TCR A2.13 alpha
E: T-CELL-RECEPTOR, TCR A2.13 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,15616
Polymers94,8735
Non-polymers1,28311
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16210 Å2
ΔGint-89 kcal/mol
Surface area35420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.803, 106.695, 132.962
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
MHC class II HLA-DQ- ... , 2 types, 2 molecules AB

#1: Protein MHC class II HLA-DQ-alpha chain / DQA1*03:01 (DQ8-alpha chain)


Mass: 21124.516 Da / Num. of mol.: 1 / Mutation: I75C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Skin, lymphoid, lungs, stomach and intestines / Cell: B Lymphocytes, dendritic cells, macrophages / Gene: HLA-DQA1 / Organ: Parenchyma / Plasmid: pZip3 / Cell (production host): cabbage looper ovarian / Cell line (production host): High Five (BTI-Tn-5B1-4) / Organ (production host): ovary / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B / References: UniProt: Q30069
#2: Protein MHC class II HLA-DQ-beta-1 / DQB1*03:02 (DQ8-beta chain)


Mass: 22605.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Class II histocompatibility antigen, alpha domain / Source: (gene. exp.) Homo sapiens (human) / Tissue: Skin, lymphoid, lungs, stomach and intestines / Cell: B Lymphocytes, dendritic cells, macrophages / Gene: HLA-DQB1 / Organ: Parenchyma / Plasmid: pZip3 / Cell line (production host): High Five (BTI-Tn-5B1-4) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B / References: UniProt: O19707

-
T-CELL-RECEPTOR, TCR A2.13 ... , 2 types, 2 molecules DE

#4: Protein T-CELL-RECEPTOR, TCR A2.13 alpha


Mass: 22633.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Islets of Langerhans / Cell: Beta cells / Gene: TRAV26-1*01 / Organ: Pancreas / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli (E.coli)
#5: Protein T-CELL-RECEPTOR, TCR A2.13 beta


Mass: 27076.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Islets of Langerhans / Cell: Beta cells / Gene: TRBV5-1*01 / Organ: Pancreas / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli (E.coli)

-
Protein/peptide / Sugars , 2 types, 3 molecules C

#3: Protein/peptide Hybrid insulin peptide (HIP; InsC8-15-NPY68-74)


Mass: 1433.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Islets of Langerhans / Cell: Beta cells / Organ: Pancreas / Plasmid: pZip3 / Cell (production host): cabbage looper ovarian / Cell line (production host): High Five (BTI-Tn-5B1-4) / Organ (production host): ovary / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): DH10B
#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.: 2 / 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

-
Non-polymers , 3 types, 154 molecules

#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Potassium sodium tartrate, 14% PEG 20,000 with seeding C8 silver bullet (Hampton Research)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.6→49.51 Å / Num. obs: 30434 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 33.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.046 / Rrim(I) all: 0.112 / Net I/σ(I): 16.5
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 3659 / CC1/2: 0.982 / Rpim(I) all: 0.109

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
autoXDSdata reduction
Coot0.9.8.92model building
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.51 Å / SU ML: 0.2777 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4641
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.225 1425 4.69 %
Rwork0.1845 28948 -
obs0.1865 30373 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 0 78 145 6519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026526
X-RAY DIFFRACTIONf_angle_d0.49268887
X-RAY DIFFRACTIONf_chiral_restr0.0439981
X-RAY DIFFRACTIONf_plane_restr0.00361149
X-RAY DIFFRACTIONf_dihedral_angle_d12.01042321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.29561240.22922855X-RAY DIFFRACTION99.97
2.69-2.80.25191370.22262853X-RAY DIFFRACTION100
2.8-2.930.2951450.2242835X-RAY DIFFRACTION100
2.93-3.080.24821340.22952890X-RAY DIFFRACTION100
3.08-3.280.26831460.20862843X-RAY DIFFRACTION100
3.28-3.530.25451450.19262877X-RAY DIFFRACTION100
3.53-3.880.2361460.18242870X-RAY DIFFRACTION99.97
3.88-4.440.17611440.14952918X-RAY DIFFRACTION100
4.45-5.60.16641590.13912932X-RAY DIFFRACTION100
5.6-49.510.21271450.18583075X-RAY DIFFRACTION99.94
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)
13.8004332733-2.547037284272.014061509252.11014768361-0.5284252646524.018411116570.0687645929149-0.0713243906044-0.204984313528-0.02353810945920.0896807184559-0.07235787693830.316912873624-0.203028441671-0.1772657926290.233207372564-0.00688940943297-0.004541401050390.180181020471-0.06183083239250.2712282950251.0178.62914.323
21.86633493811-2.7165643276-0.8105055488664.119962806440.5586101870922.8810247110.2718138820430.04398881667740.115940468113-0.06342044548980.112308001825-0.2995744180770.07476271789290.603603178176-0.3890525082210.301414617362-0.02115786704910.02104372550160.252094901156-0.1266812169230.31455322697710.83411.84512.454
32.91414377433-0.2858737890084.678358985715.368944300340.8309042904298.80513147403-0.1715549879570.6349510864230.468599050664-0.4836628657740.0657979273842-0.38850269435-0.6595471005240.6772362293360.05700632880930.28644401957-0.03013394400080.0223921788560.234067025047-0.02950217262920.2844414868138.64920.3019.566
48.21834215693-1.149714873134.059831859723.59688578311-2.481756983253.91469966302-0.7236408023630.4619274282631.41018875192-0.0226698283752-0.265313230987-0.152828512818-1.18443545107-0.4290325547570.6311269551470.4595168565490.0256780636612-0.04860636964680.2627177327870.03219464659220.395285154222.05327.69210.3
51.69286300829-1.089166382070.5482503891036.277911364440.06918696431262.71763176970.212706091130.110495646306-0.309474371051-0.007484251765360.0575068864271-0.2761031770360.2853663218520.328016968999-0.2359471958350.1688927485620.0212776516655-0.09909314455290.201612139838-0.07040148458280.30289469275614.758.67923.98
60.538529335135-0.6625757420071.390189892940.894698746994-1.978654187354.632130101380.4307319629140.0448067071326-0.128717374069-0.3145570482810.1317140011490.03703543043941.12437116420.46069616791-0.3959265501330.6500630656610.18546213734-0.2263065529590.327216567825-0.188076731420.51088694834615.265-6.49512.71
77.26199061602-1.260478017380.1342836766074.605978297113.411408176355.4903090463-0.1271663028290.939592161170.389508705923-0.5047550397550.113909058232-0.298680097834-0.1904221835170.344104665134-0.130869058940.290356437187-0.0448819754031-0.004999057239360.329361392853-0.02628076489320.1324178014794.39511.413-14.538
82.80876532386-1.504967427722.961729727772.95908160263-2.344900860177.695880705950.2353269674410.2272059641520.179381151352-0.158224818714-0.100539162428-0.2433095603420.8000970342180.880375371071-0.1949614996240.3611891649730.0772427333807-0.02009569991620.405787767034-0.143739247980.25512680039311.96.908-3.152
92.583933040941.02525405158-0.9840123113973.30755868923-3.204365517786.16599993287-0.1438404897650.334122247259-0.414387712829-0.174597459533-0.224963914771-0.7505492525020.3826267247040.3655163474430.3345478257790.2961345492920.013102442614-0.06061962612220.419828661628-0.1639439583410.40956972059911.2418.6370.265
103.06210907513-0.8501391501150.9426786769195.39237739841-0.7194070662413.463307643060.03133821566891.274394719290.0593035390014-0.694685629077-0.0489228599173-0.652797190160.5807105756351.795288303360.218936983690.3815189922780.08006988223470.08031075106080.860435657174-0.1167761160090.43061132205412.93710.763-12.092
110.220220878081-0.06971236513630.6472100283790.0183301920079-0.1981799557841.995654120140.08743116408270.370804171905-0.0289860101949-0.2549799534010.186160574361-0.2072934068830.3599450971440.634119319298-0.1461251203570.9482554499180.598703662838-0.001322977561070.823684819902-0.5012913051560.16560521086215.888-0.356-6.369
121.247690097940.244887079381-0.103381712951.959610735770.0352170342923.502510645910.3631642384460.402885373614-0.0269743434579-0.0352553918292-0.105085114429-0.2566499626120.2817498920050.27674303098-0.1617771776220.237178376290.0340800541862-0.04051142062020.162613426875-0.06992597629830.2571701317548.0563.94715.301
137.25103698676-6.059802978711.492856660818.7764827047-0.6245350404044.976666275360.383425946953-0.201396761586-0.286523795701-0.133428175005-0.09317858383020.4476106681070.280277620833-0.667812622345-0.2731362098670.269059032941-0.0945253514424-0.03203310231880.166027806646-0.01025264014830.248458294076-5.3627.80220.048
143.03292930021-1.58320904488-0.9450139807014.19292827031.424522420692.957034723340.0902902186882-0.0842758516056-0.5444351029920.2775985108930.2002077178320.1728236739810.584550010462-0.224442860292-0.2307753196870.288963595066-0.0380836325356-0.14257021980.1343869328740.04784887046870.4214555388132.3880.4727.935
158.79291196684-1.089553555573.117334720915.46451115002-5.683855652876.81043659949-0.183803879141-0.588339132020.6250926858090.5250353003890.0869715571346-0.529250983356-0.65209021339-0.4074548190270.1004865436430.2233578439780.0587243900793-0.02574775745990.244078771491-0.0432104666540.236401941816-1.69513.41531.517
161.47210442545-0.2409893133792.200273369441.952327165351.803398392185.64492303821-0.261328323787-0.1697383059880.349069329932-0.1193327030570.2142993095290.29154219176-1.06068068388-0.9461124720720.1553154790120.2879495871760.0624650700018-0.0121547456270.223990862260.005453703587870.367141462701-7.96321.8079.778
173.273623713290.8770237029841.971865426553.425542219411.974950344995.5912545204-0.01664362292570.3494318334780.315938961048-0.5411880774570.0329791830710.276649017147-0.195247620367-0.100587769305-0.04957211271640.3516540635980.0180599254436-0.03800707555580.2115823122780.06887457959230.198075363394-10.0888.263-12.942
183.36314845701-0.5813041277980.3294022822211.42899826946-1.386935576331.358491997330.04062511480040.5559493001030.140617109107-0.673913188049-0.2913037952580.4641967533060.180048088186-0.5581671644590.2377068680250.7032834964740.0949844428932-0.1989321269810.4366669851330.09757699798750.267870005901-16.3938.164-22.386
191.55568850567-0.1470692036431.049521753141.259158272961.032602531614.431223410330.2264910761210.2939370591630.27702448746-0.741928556282-0.405235882956-0.0116329521743-0.969898669843-0.808943190290.1357333855070.5410122436750.125920283672-0.1139152771940.2555714972930.0884325020440.374876354974-15.36715.662-18.995
207.82158360723-4.19286332507-1.541763728545.405019882934.318969142674.169795845780.2775148285110.6121772446670.632236751549-0.3021538240790.2445557695720.466316879028-1.61755618972-0.776418442136-0.3128015385910.4807666287530.1228740741960.009277913872510.275513870193-0.01930283410080.3730672657720.96626.15419.847
212.11001429452-0.540037829971.306453136522.7098226358-1.50830437422.684552733740.6244532100090.0935970633887-0.2482121425960.72530034944-0.286945830958-0.630170643635-0.1036662235640.8062175488910.04078846273640.3014733538170.0485947018144-0.1281909294210.2781373799660.0501719443790.50491958672410.9137.13929.609
221.957720820750.9205978814371.190182581712.988829066310.5583260734061.49901543311-0.161453207676-0.02527683651560.260995895931-0.29348166724-0.13979510.149012286502-1.15405131755-0.172457667360.2564013427180.3950759065340.112361291121-0.004645835939610.209875866360.005578946219960.312532274939-2.27636.22140.912
234.88393288834-0.1392932954690.2071490693353.734028735551.098041324076.398538896420.104590896278-0.05237746848550.1132488738680.117497349582-0.01108942290580.134542162681-0.236626728881-0.369816975791-0.02919073779140.1971669021240.04166148203970.045559420770.05899797334610.02232286670440.1867181955370.91326.33943.199
241.672945666580.1096099253270.1493392334911.350409558451.588054333053.931189162160.254147688577-0.05622804951510.0583551426798-0.0786046205316-0.103340542863-0.0737814176516-0.471481169368-0.34814497475-0.0483781764660.2606020876420.07506509563820.03192661383590.1530730843380.02822299264020.2298878008351.18130.99440.734
252.250186896062.4926529643.508397644693.962638386944.569565847215.835718582250.0198619409274-0.4518027816160.114394165225-0.197573812271-0.4587510154030.173094018358-0.478594745679-0.9440581924640.5169503317430.3243237377650.0548896092189-0.0511770098820.277949216766-0.04423220745220.2360824223112.87744.16765.496
268.65684841283-3.106608194122.886266876425.95875745926-1.243712394288.4088239844-0.366221254087-0.709944982840.43878296810.1794650482240.290606578306-1.177680256-0.04862994342880.7243498832250.08394143481250.3530506969150.000520836966226-0.06575219680910.260942394149-0.04399895561850.41927135480621.54147.22774.485
278.478896713897.04832345738-5.9866747727.31042315803-3.568370686376.17830340418-0.1796100124430.7562757046780.708673200737-0.304949014480.171571156813-0.373562223167-0.620221488284-0.0729205404703-0.01778332282320.5332747143220.0251366997346-0.09326420251020.4154368081510.107745055220.46659677517110.74752.54363.423
285.650748413666.29323739692-1.14290588619.55173074717-1.703704951354.88551999353-0.3125734055610.00186262428452-0.419227151579-0.5632195436940.208436928776-0.0023097114344-0.0877842274386-0.2575880347110.1171892577160.2415807082350.0641439428979-0.002379082441850.221383293529-0.02859448762460.22022967747710.37141.73667.493
295.99907236144-0.761453008259-2.372278306511.998216998970.03615573511662.06371204005-0.236493607354-0.3372462132861.89911657055-0.1664656428710.445967145457-0.779446546608-0.7006622339380.4378976946480.01971734774850.492839016161-0.0561625675449-0.03632186484230.310701838647-0.07381436981830.59303154638418.70457.06970.977
304.302193540463.311065610391.159545047775.015107573471.757421682312.268595861190.147431621940.02880621761710.01465107570960.199099627771-0.0164162690879-0.2196715177420.1308439764710.441446648617-0.09501443254630.132062403066-0.0134324438882-0.01708810933510.200760783371-0.01154667779490.28932917523326.28423.90943.421
312.30682113570.9425287508650.4369807446072.550631770130.7633720057833.201781415310.1159867208140.130951448679-0.053661997558-0.2699363698890.130058588829-0.111576990524-0.2061805304050.316388414548-0.2329524413960.198410070953-0.02813162159110.02720530486920.171782591107-0.02895822641950.17888998017921.29424.80735.289
322.21885312024-0.0147715640402-0.08401029864580.491338499782-0.310018926513.32296051984-0.164259937043-0.4021230310990.47669561562-0.2815092936350.1729385128470.0182452923468-0.7918436360480.38851803746-0.01107626174050.232185767315-0.239505096599-0.02554912791830.259754313733-0.05945974611090.42773707949933.41238.61649.879
331.741097700810.474686395018-2.114276232591.9096573239-0.4074973454884.94679992195-0.09239514032610.0648507758841-0.0300831649710.01615177207530.0518092096576-0.0675726958663-0.191434320846-0.1499915831380.0284944847440.134764299682-0.0296087507307-0.05357508207740.214217766884-0.03234789863620.16351808816719.61238.89170.532
343.789010749810.455857140056-0.5118839264333.94395424157-0.8690532588934.63461611129-0.2023901090.4761831470050.364213495394-0.6067244694850.312915722193-0.263064149559-0.213413548483-0.227137095647-0.05609257329440.322555438284-0.009572159002280.05851567068640.226406652873-0.03043292214680.21048195621721.06839.74261.386
353.933222676810.254014078303-3.265504939291.13012328657-0.5477508792575.67740690108-0.3751428645750.000797344951917-0.1809902126810.06954808863050.0322479092797-0.2188156475940.177133718540.2175249673130.1974601694890.192596353573-0.0417533357166-0.06421747148020.150010743392-0.02774960585710.2301172315826.97333.82668.311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:15 )A0 - 15
2X-RAY DIFFRACTION2( CHAIN A AND RESID 16:26 )A16 - 26
3X-RAY DIFFRACTION3( CHAIN A AND RESID 27:45 )A27 - 45
4X-RAY DIFFRACTION4( CHAIN A AND RESID 46:55 )A46 - 55
5X-RAY DIFFRACTION5( CHAIN A AND RESID 56:76 )A56 - 76
6X-RAY DIFFRACTION6( CHAIN A AND RESID 77:87 )A77 - 87
7X-RAY DIFFRACTION7( CHAIN A AND RESID 88:101 )A88 - 101
8X-RAY DIFFRACTION8( CHAIN A AND RESID 102:122 )A102 - 122
9X-RAY DIFFRACTION9( CHAIN A AND RESID 123:146 )A123 - 146
10X-RAY DIFFRACTION10( CHAIN A AND RESID 147:166 )A147 - 166
11X-RAY DIFFRACTION11( CHAIN A AND RESID 167:178 )A167 - 178
12X-RAY DIFFRACTION12( CHAIN B AND RESID 1:18 )B1 - 18
13X-RAY DIFFRACTION13( CHAIN B AND RESID 19:32 )B19 - 32
14X-RAY DIFFRACTION14( CHAIN B AND RESID 33:64 )B33 - 64
15X-RAY DIFFRACTION15( CHAIN B AND RESID 65:77 )B65 - 77
16X-RAY DIFFRACTION16( CHAIN B AND RESID 78:97 )B78 - 97
17X-RAY DIFFRACTION17( CHAIN B AND RESID 98:162 )B98 - 162
18X-RAY DIFFRACTION18( CHAIN B AND RESID 163:177 )B163 - 177
19X-RAY DIFFRACTION19( CHAIN B AND RESID 178:191 )B178 - 191
20X-RAY DIFFRACTION20( CHAIN C AND RESID -2:2 )C-2 - 2
21X-RAY DIFFRACTION21( CHAIN C AND RESID 3:12 )C3 - 12
22X-RAY DIFFRACTION22( CHAIN D AND RESID 2:37 )D2 - 37
23X-RAY DIFFRACTION23( CHAIN D AND RESID 38:80 )D38 - 80
24X-RAY DIFFRACTION24( CHAIN D AND RESID 81:119 )D81 - 119
25X-RAY DIFFRACTION25( CHAIN D AND RESID 120:137 )D120 - 137
26X-RAY DIFFRACTION26( CHAIN D AND RESID 138:152 )D138 - 152
27X-RAY DIFFRACTION27( CHAIN D AND RESID 153:167 )D153 - 167
28X-RAY DIFFRACTION28( CHAIN D AND RESID 168:192 )D168 - 192
29X-RAY DIFFRACTION29( CHAIN D AND RESID 193:204 )D193 - 204
30X-RAY DIFFRACTION30( CHAIN E AND RESID 3:37 )E3 - 37
31X-RAY DIFFRACTION31( CHAIN E AND RESID 38:118 )E38 - 118
32X-RAY DIFFRACTION32( CHAIN E AND RESID 119:133 )E119 - 133
33X-RAY DIFFRACTION33( CHAIN E AND RESID 134:171 )E134 - 171
34X-RAY DIFFRACTION34( CHAIN E AND RESID 172:197 )E172 - 197
35X-RAY DIFFRACTION35( CHAIN E AND RESID 198:253 )E198 - 253

+
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