[English] 日本語
Yorodumi
- PDB-7sr5: Single chain trimer HLA-A*02:01 (Y108C, A163C) with Wilms tumor p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sr5
TitleSingle chain trimer HLA-A*02:01 (Y108C, A163C) with Wilms tumor protein peptide RMFPNAPYL
Components
  • VHH
  • Wilms tumor protein peptide,Beta-2-microglobulin,MHC class I antigen chimera
KeywordsIMMUNE SYSTEM / HLA / VHH / HPV / SCT
Function / homology
Function and homology information


posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / negative regulation of female gonad development / positive regulation of heart growth / visceral serous pericardium development ...posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / negative regulation of female gonad development / positive regulation of heart growth / visceral serous pericardium development / Nephron development / glomerular basement membrane development / diaphragm development / mesenchymal to epithelial transition / sex determination / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / positive regulation of male gonad development / cellular response to gonadotropin stimulus / gonad development / Transcriptional regulation of testis differentiation / tissue development / podocyte differentiation / double-stranded methylated DNA binding / cardiac muscle cell fate commitment / hemi-methylated DNA-binding / male genitalia development / glomerulus development / camera-type eye development / C2H2 zinc finger domain binding / ureteric bud development / branching involved in ureteric bud morphogenesis / adrenal gland development / negative regulation of gene expression via chromosomal CpG island methylation / antigen processing and presentation of peptide antigen via MHC class I / germ cell development / vasculogenesis / cellular response to cAMP / epithelial cell differentiation / RNA splicing / kidney development / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / negative regulation of cell growth / MHC class I protein complex / positive regulation of miRNA transcription / recycling endosome membrane / phagocytic vesicle membrane / male gonad development / heart development / early endosome membrane / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / negative regulation of translation / nuclear speck / immune response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Wilm's tumour protein, N-terminal / Wilm's tumour protein / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type ...Wilm's tumour protein, N-terminal / Wilm's tumour protein / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin / Wilms tumor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Pongo pygmaeus (Bornean orangutan)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFinton, K.A.K. / Rupert, P.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Front Immunol / Year: 2023
Title: Effects of HLA single chain trimer design on peptide presentation and stability.
Authors: Finton, K.A.K. / Rupert, P.B. / Friend, D.J. / Dinca, A. / Lovelace, E.S. / Buerger, M. / Rusnac, D.V. / Foote-McNabb, U. / Chour, W. / Heath, J.R. / Campbell, J.S. / Pierce, R.H. / Strong, R.K.
History
DepositionNov 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Wilms tumor protein peptide,Beta-2-microglobulin,MHC class I antigen chimera
B: VHH
C: Wilms tumor protein peptide,Beta-2-microglobulin,MHC class I antigen chimera
D: VHH


Theoretical massNumber of molelcules
Total (without water)120,4414
Polymers120,4414
Non-polymers00
Water4,053225
1
A: Wilms tumor protein peptide,Beta-2-microglobulin,MHC class I antigen chimera
B: VHH


Theoretical massNumber of molelcules
Total (without water)60,2202
Polymers60,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Wilms tumor protein peptide,Beta-2-microglobulin,MHC class I antigen chimera
D: VHH


Theoretical massNumber of molelcules
Total (without water)60,2202
Polymers60,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.476, 117.476, 261.269
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Wilms tumor protein peptide,Beta-2-microglobulin,MHC class I antigen chimera / WT33


Mass: 47683.484 Da / Num. of mol.: 2 / Mutation: Y108C, A163C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pongo pygmaeus (Bornean orangutan)
Gene: WT1, B2M, HLA-A / Production host: Homo sapiens (human)
References: UniProt: P19544, UniProt: P16213, UniProt: A0A678ZGP6
#2: Antibody VHH


Mass: 12536.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 200 mM NH4Citrate, 14.5% PEG 3350

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 76503 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 40.97 Å2 / CC1/2: 0.997 / Net I/σ(I): 16.8
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 7530 / CC1/2: 0.772

-
Processing

SoftwareName: PHENIX / Version: 1.19.1_4122 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SR0

7sr0


Resolution: 2.35→48.74 Å / SU ML: 0.2797 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.0818
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2481 3825 5 %
Rwork0.2294 72678 -
obs0.2304 76503 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.08 Å2
Refinement stepCycle: LAST / Resolution: 2.35→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7279 0 0 225 7504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00177464
X-RAY DIFFRACTIONf_angle_d0.478710155
X-RAY DIFFRACTIONf_chiral_restr0.03951077
X-RAY DIFFRACTIONf_plane_restr0.00421326
X-RAY DIFFRACTIONf_dihedral_angle_d4.84871051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.30051490.29022603X-RAY DIFFRACTION99.1
2.38-2.410.31521440.28592661X-RAY DIFFRACTION100
2.41-2.440.30071470.27382678X-RAY DIFFRACTION99.96
2.44-2.480.30251470.26642638X-RAY DIFFRACTION99.71
2.48-2.520.27291320.26022656X-RAY DIFFRACTION99.68
2.52-2.550.26891340.25442687X-RAY DIFFRACTION100
2.55-2.60.2621440.24042661X-RAY DIFFRACTION100
2.6-2.640.26251320.25492659X-RAY DIFFRACTION99.96
2.64-2.690.3131470.26422672X-RAY DIFFRACTION99.96
2.69-2.740.31231340.26642683X-RAY DIFFRACTION99.89
2.74-2.80.30671370.26822680X-RAY DIFFRACTION99.89
2.8-2.860.291280.27122698X-RAY DIFFRACTION99.82
2.86-2.920.30421390.26542685X-RAY DIFFRACTION99.86
2.92-30.24761390.24532662X-RAY DIFFRACTION99.75
3-3.080.30241370.24682682X-RAY DIFFRACTION99.09
3.08-3.170.26581470.23882672X-RAY DIFFRACTION99.68
3.17-3.270.2581540.24532677X-RAY DIFFRACTION99.72
3.27-3.390.26631470.24592687X-RAY DIFFRACTION99.75
3.39-3.520.28521440.24512685X-RAY DIFFRACTION99.61
3.52-3.680.22691460.22092694X-RAY DIFFRACTION99.4
3.68-3.880.21191280.20722718X-RAY DIFFRACTION99.48
3.88-4.120.22451570.19832663X-RAY DIFFRACTION98.5
4.12-4.440.22041470.18212712X-RAY DIFFRACTION99
4.44-4.880.17441280.17182769X-RAY DIFFRACTION99.14
4.89-5.590.19961430.19722733X-RAY DIFFRACTION98.8
5.59-7.040.23191460.24182756X-RAY DIFFRACTION97.97
7.04-48.740.25991480.24732907X-RAY DIFFRACTION97.17
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)
10.2628334336260.3936835192990.08216937666250.3579475090940.144593514494-0.0603760644844-0.239178865913-0.004307428069240.34861321441-0.0196983209288-0.05560075528820.07230307023920.00366537980770.0195807071459-0.005258267454280.183983357764-0.00360916044718-0.03654375476670.286591829475-0.04375704307670.326296002504-9.8269753141635.9566610207-29.1522997361
20.8278927653780.2019884159040.2429454654060.262005677382-0.1164924872180.104834809263-0.1979699351060.1515581674530.197033785122-0.007658361952970.1026449251320.04708008300820.07568423098680.111239547607-3.20545607673E-50.282922944243-0.0944648025792-0.0186604875630.3486475651550.02212043387890.260510071489-12.240449207127.628623743-46.7237754243
30.430074022119-0.182061886502-0.09357575593490.378561258880.101305199652-0.0782191837289-0.245662345966-0.007413191662840.660659940425-0.00623613619517-0.01307333614420.208679239876-0.05103194823080.0498709240834-0.004990344396270.298319773101-0.0913795556359-0.05797654097880.3540566383890.03045230601560.337660694415-13.202017115534.0029445941-39.6834849369
40.330394545151-0.2050229177650.1493480924820.3927948934450.09343350232640.170569950064-0.0825908367572-0.0238308212245-0.264654104804-0.279680030212-0.02072734050220.01107927128370.270066686905-0.0123377317024-2.15787905691E-50.32868775477-0.0249755857258-0.01995210494940.2849211728080.03017389795730.356964894015-0.62660284323328.0237202976-30.7565052903
50.6083134795940.5239689284490.6774763419310.8444447472850.1415994980640.761015292011-0.0187376795786-0.6455307232960.5090510738280.106389241327-0.2007657195020.04172843377640.0269404074933-0.137038444713-0.05041833037360.251104099856-0.00997037477661-0.02626099956940.492490195756-0.1791018447930.355614648431-5.5780529138340.7256142865-19.5513691345
60.195607260193-0.0867646873399-0.2247477189860.1140883412980.2417217935240.593504438772-0.2553177188620.07400884628240.364110232073-0.1324918058230.1511609757650.05810079101070.2769734842530.152123640427-0.01315766539930.307313069826-0.0727591998974-0.06553913223640.3059220254080.03002364434650.37573209062710.389565329642.1928646735-37.2353824037
70.212638536676-0.259133938705-0.2995351430050.2789395081820.2225922009080.15855392071-0.2118674723170.169196400480.573828293525-0.05339085522410.1624876195210.284377971764-0.2261749438250.0207860629977-0.001890322719720.418411875419-0.142595155775-0.2559418714220.3735874174820.2077649729690.670466641303-11.002999344249.0489323366-54.5434222661
80.07204406689210.0899511987373-0.03711025271020.1300537329830.0633926024310.0866483914001-0.228733984347-0.0783622890189-0.203208200160.113961010294-0.03363060450230.420971381713-0.02219708913870.0681610363977-0.009204126730290.3049559929690.01743393797350.0134978894520.3445245894790.05253079594660.37626357685-37.83208627779.07206594772-38.755584878
90.0370153313097-0.0369754167483-0.09231976600530.02006499721890.0448511984120.0482605063094-0.1710700146550.532482172408-0.325220174162-0.232415458650.0702030932565-0.00995435853509-0.09324130479990.0775087089759-3.91887031801E-50.397359922908-0.1527897628440.01851002443140.538202318361-0.03384869680420.379952834772-32.148420219410.1509175698-50.7683575545
100.4176127689910.278570121097-0.02946779650140.144114549349-0.0440169780868-0.00497526528525-0.133792410679-0.03067597777780.0822276693167-0.1124373746790.164556647413-0.1472206303240.0332186544757-0.0173745871448-2.11142317501E-50.288172435198-0.02015811868260.04973308354060.3095309232370.01646991391990.319925597244-25.95550122712.3663686899-41.1463634849
110.4590167697060.1915308624460.09636164067170.159715669407-0.1153348840930.169675445635-0.121066440701-0.0233647405546-0.05557936642470.04238313125520.09632690321720.1705883429930.0004652244669450.0564563635206-9.96314441056E-60.304315396492-0.006660771680970.02519291142690.28241805780.04112035172610.293921883774-32.109241640913.6639862928-40.8894591117
121.3396591675-0.681973576539-0.5874971333240.5470541351690.117711221714-0.149152387531-0.299109239125-0.309494665688-0.3557539059370.07525300478410.1761269854410.1294024912160.04433608764410.137096639009-0.0364858058820.345162096070.1364202434540.06585263575190.4073024505020.06225585715520.277325543664-13.957316255986.3735836685-23.9322383917
132.07828794884-1.44250731137-0.588442939380.8506604667820.03311523999750.842310720868-0.1898348734970.189326180848-0.2485046184610.07301734352710.06183741286430.139129823829-0.1985663787940.0139493765923-0.01761998591420.298542049720.03690255557090.02424232235310.292220417012-0.006516975600240.317284645263-4.169457917479.6834456517-39.5721166053
140.6367906293910.2752027847580.5207321860670.2846511186790.4223749216850.596915143462-1.22558891204-0.0840002543563-1.30178554354-0.06192652839850.4630207470380.3698849625010.3784084879851.02302628786-0.4644327777320.6292259486990.6426252985140.6366829721530.5593017673310.2773710327650.870281231036-7.8945339304169.4167143243-14.2298604493
150.00103474528039-0.02021405117810.001729889134490.0186374232745-0.01972270477380.02374000323390.287002768906-0.272757458091-0.027016529433-0.00692929586793-0.06770181103050.02205675788030.04912794638840.0215889975412-0.0001264745954450.3787311534420.02539692721070.03634762435310.4579819020360.06023842627030.298627841928-39.9752567815101.821615352-14.3584312315
160.00930893798886-0.00674293555443-0.02067292041130.01267625846910.01544677043130.01821993549720.1842019560570.3664317706320.379322991021-0.1184205042010.0123154564770.0997138257332-0.1623946065610.0471333820504-0.0001386024596260.302283180672-0.026317608958-0.04922282133760.4079457121050.1412625782390.464265567639-40.114208756113.134809057-33.7941392306
170.001283783756130.0100503857849-0.0113973851466-0.0282070450265-0.02818751792860.0202865019062-0.10266410378-0.5285909470.2738026379610.1576471249660.0883744449219-0.056143987643-0.133520551769-0.02849854506974.35511177861E-50.3530932912050.1087994788660.06440481417710.459563491640.04060570989540.395131776218-37.5623268827108.890468959-18.5733764851
180.2419742540640.218918269132-0.01988152538020.4148483120310.1910287932090.159926806638-0.130816095364-0.247102726698-0.109819641571-0.09029081353880.3191778831520.0981364377061-0.180700339429-0.218598386411-0.004824810881690.2790223037890.0783796910404-0.02741566726370.4285241914160.05149968320270.356944698519-31.553328697499.5063518347-19.0108410897
190.02990094482480.00889684905148-0.01382404814180.00450660900919-0.02022383647870.0217914441542-0.0917244038603-0.01503776770450.101078240623-0.0464710376702-0.106965882713-0.2693200011360.226878192784-0.0302638402278-0.0004611547832240.2742794776210.0349366479431-0.02905584613350.38078430295-0.03150287463470.30837054064-25.3492582162104.517988244-19.575314584
200.0382765101252-0.01453464435640.00192242936820.0150902932764-0.007167243466560.00217339859291-0.06056355248310.2674794375160.2636440115680.2009864891420.221366198516-0.0430494919840.1453797804630.0932232926954-6.56032762281E-50.2809363425420.0037102568919-0.02719607840420.452176094672-0.0204973417340.340903048187-23.8540233243107.397171646-28.5080852889
210.02163259112910.03039614935550.006815249351910.0406934700502-0.003717801015030.001159964945240.0536137154945-0.3195286241930.342665803605-0.1948099223130.120690988346-0.0409152891931-0.205127557189-0.09763662108110.0002720450754480.347756970670.0294585687593-0.01502131955130.420189873928-0.03769529846620.325099228338-29.9553390787111.516511577-16.5504530074
220.03907525946550.0350749819191-0.0166579753970.0217970622474-0.01157704766210.000438579709687-0.1155751166150.02674891402850.4951752582920.115904284222-0.00284315043095-0.02475062846080.0535960371112-0.009858814219417.81018159869E-50.3117029025640.07316577894540.01172112340330.33229539002-0.03671929958970.450674895575-33.4358869316110.874851722-19.3575625197
230.0461100471879-0.002703469061590.006745960398810.0104250677795-0.01452446300390.0129302525534-0.3766544494670.351541514477-0.06833190899320.01579481615010.0234046357254-0.1641019837570.216139989414-0.03507483362530.0003258668339470.3720774512860.0187988906903-0.02352027411770.3502814991160.03578027223050.351632319784-33.3845951927108.965594731-36.0641845721
240.1337413830750.0589627010625-0.06185963656910.216282429750.01617504084250.045566578183-0.332822513934-0.410640899766-0.165067815186-0.08826382682850.3010340943530.2465417163190.0778466658625-0.1924234712530.0001237512892670.3547954456650.1176283534740.01005190930910.3978398445490.06217871191020.219134917706-32.957750836197.4493464802-17.1897913988
25-0.005972506269790.0126148020720.01434178451920.00907708053877-0.01243294137090.0254723706568-0.2250768528940.4146313903680.0483664900912-0.009625075185530.407060619259-0.06340581001160.2191341493460.1777767471599.96827016523E-50.297258163438-0.0215296606433-0.03810630412890.4059644848180.07448172577560.336237746863-40.9710049366106.023922003-32.8803977565
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 35 )AA1 - 351 - 23
22chain 'A' and (resid 36 through 107 )AA36 - 10724 - 95
33chain 'A' and (resid 108 through 155 )AA108 - 15596 - 121
44chain 'A' and (resid 156 through 199 )AA156 - 199122 - 165
55chain 'A' and (resid 200 through 305 )AA200 - 305166 - 271
66chain 'A' and (resid 306 through 328 )AA306 - 328272 - 294
77chain 'A' and (resid 329 through 417 )AA329 - 417295 - 379
88chain 'B' and (resid 3 through 19 )BB3 - 191 - 17
99chain 'B' and (resid 20 through 35 )BB20 - 3518 - 33
1010chain 'B' and (resid 36 through 77 )BB36 - 7734 - 73
1111chain 'B' and (resid 78 through 117 )BB78 - 11774 - 113
1212chain 'C' and (resid 1 through 155 )CC1 - 1551 - 121
1313chain 'C' and (resid 156 through 349 )CC156 - 349122 - 306
1414chain 'C' and (resid 350 through 417 )CC350 - 417307 - 350
1515chain 'D' and (resid 3 through 9 )DD3 - 91 - 7
1616chain 'D' and (resid 10 through 19 )DD10 - 198 - 17
1717chain 'D' and (resid 20 through 27 )DD20 - 2718 - 25
1818chain 'D' and (resid 28 through 47 )DD28 - 4726 - 42
1919chain 'D' and (resid 48 through 58 )DD48 - 5843 - 53
2020chain 'D' and (resid 59 through 68 )DD59 - 6854 - 63
2121chain 'D' and (resid 69 through 77 )DD69 - 7764 - 72
2222chain 'D' and (resid 78 through 84 )DD78 - 8473 - 79
2323chain 'D' and (resid 85 through 92 )DD85 - 9280 - 87
2424chain 'D' and (resid 93 through 111 )DD93 - 11188 - 106
2525chain 'D' and (resid 112 through 117 )DD112 - 117107 - 112

+
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