[English] 日本語
Yorodumi
- PDB-6vm9: T4H2 T cell receptor bound to HLA-A2 presenting gp100T2M peptide ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vm9
TitleT4H2 T cell receptor bound to HLA-A2 presenting gp100T2M peptide (IMDQVPFSV)
Components
  • Beta-2-microglobulin
  • MHC class I antigen, A-2 alpha chain
  • Melanocyte protein PMEL
  • T4H2 T cell receptor alpha chain
  • T4H2 T cell receptor beta chain
KeywordsIMMUNE SYSTEM / TCR / MHC class I / HLA A2 / melanoma
Function / homology
Function and homology information


cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / multivesicular body, internal vesicle / melanosome organization / multivesicular body membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding ...cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / multivesicular body, internal vesicle / melanosome organization / multivesicular body membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / melanosome / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / MHC class I, alpha chain, C-terminal ...PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / MHC class I antigen / Melanocyte protein PMEL / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSmith, A.R. / Baker, B.M.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner
Authors: Smith, A.R. / Alonso, J.A. / Ayres, C.M. / Singh, N.K. / Hellman, L.M. / Baker, B.M.
History
DepositionJan 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: 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.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanocyte protein PMEL
D: T4H2 T cell receptor alpha chain
E: T4H2 T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)94,9655
Polymers94,9655
Non-polymers00
Water00
1
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanocyte protein PMEL

D: T4H2 T cell receptor alpha chain
E: T4H2 T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)94,9655
Polymers94,9655
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)129.744, 129.744, 113.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

-
Components

#1: Protein MHC class I antigen, A-2 alpha chain


Mass: 31854.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: A0A5B8RNS7, UniProt: A0A140T913*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P61769
#3: Protein/peptide Melanocyte protein PMEL / ME20-M / ME20M / Melanocyte protein Pmel 17 / Melanocytes lineage-specific antigen GP100 / Melanoma- ...ME20-M / ME20M / Melanocyte protein Pmel 17 / Melanocytes lineage-specific antigen GP100 / Melanoma-associated ME20 antigen / P1 / P100 / Premelanosome protein / Silver locus protein homolog


Mass: 1035.213 Da / Num. of mol.: 1 / Fragment: epitope (UNP residues 209-217) / Mutation: T210M / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40967
#4: Protein T4H2 T cell receptor alpha chain


Mass: 22768.986 Da / Num. of mol.: 1 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV12-2, TRAC / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
#5: Protein T4H2 T cell receptor beta chain


Mass: 27427.480 Da / Num. of mol.: 1 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV19, TRBC2 / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18% v/v PEG10000, 16% v/v glycerol, 250 mM Tris pH 8.5, 60 mM sodium chloride, seeded with crushed crystals

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 24229 / % possible obs: 99.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 88 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.033 / Rrim(I) all: 0.103 / Χ2: 1.111 / Net I/σ(I): 24.2
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1125 / CC1/2: 0.864 / CC star: 0.963 / Rpim(I) all: 0.324 / Rrim(I) all: 0.943 / Χ2: 0.961 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TVB
Resolution: 2.9→42.7 Å / SU ML: 0.4764 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.716
RfactorNum. reflection% reflection
Rfree0.2501 1836 8.19 %
Rwork0.2104 --
obs0.2137 22405 92.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 103.23 Å2
Refinement stepCycle: LAST / Resolution: 2.9→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 0 0 6642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216825
X-RAY DIFFRACTIONf_angle_d0.48889271
X-RAY DIFFRACTIONf_chiral_restr0.0426964
X-RAY DIFFRACTIONf_plane_restr0.00281218
X-RAY DIFFRACTIONf_dihedral_angle_d19.53862509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.970.51061020.4061186X-RAY DIFFRACTION69.28
2.97-3.060.40221200.37921300X-RAY DIFFRACTION76.8
3.06-3.160.32941280.29861423X-RAY DIFFRACTION83.3
3.16-3.270.31571420.28741541X-RAY DIFFRACTION89.47
3.27-3.40.31311350.28151577X-RAY DIFFRACTION92.19
3.4-3.550.3461420.26031605X-RAY DIFFRACTION94.48
3.55-3.740.30421540.24811674X-RAY DIFFRACTION97.03
3.74-3.980.25261540.22971661X-RAY DIFFRACTION98.21
3.98-4.280.24571540.20121698X-RAY DIFFRACTION98.88
4.28-4.710.24091520.17271700X-RAY DIFFRACTION99.36
4.71-5.390.18241520.1721734X-RAY DIFFRACTION99.42
5.39-6.790.24051510.19831723X-RAY DIFFRACTION99.68
6.79-42.70.20921500.17561747X-RAY DIFFRACTION98.91
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)
15.150661035351.233433098771.124967968072.126898155020.9011720833042.914675199950.4616415617210.513139459849-0.738107704019-0.229781329719-0.0656160676961-0.2280783227340.3792424389690.133862967948-0.2706063780851.064185050390.365132895451-0.06331952760050.624117833368-0.1074889942580.80785615119399.9260558676-7.71802376726-33.6183556195
28.630067239350.9994628977761.62078354653.9176995786-1.443761376932.628942281570.219878071207-0.911126246544-0.5838747337140.5152026540020.008061924123640.09744357334930.244350119650.130759422319-0.2756785833441.002053270360.167673830288-0.0187664536260.811730439039-0.04009689227770.72887750065997.2881627144-8.15768544102-21.9960556934
32.34214145319-0.3770683200891.250939280740.571617573529-0.7731455546216.8240728671-0.08447763913530.2074223129-0.0407084176653-0.400013610616-0.453293846810.6715771014270.194689589031-0.5710627315360.3736071585571.200441703820.409617975521-0.1468316949250.885384132079-0.2220206694630.82964895331689.8953325494-2.5587868098-35.2892754662
43.691762667530.9266587698031.528848093711.12374440856-0.5993030115951.985771462340.3976440646390.894807539984-0.283562565246-0.122385547366-0.0180204504316-0.1788037106850.4940166431450.506130225535-0.2635206282281.176690156030.406857951818-0.05993192279550.777056248869-0.07863572579380.76994699393102.5773842860.245679126234-40.9501670174
55.71854777333-0.5014844721760.2192020698945.215501103821.926527831333.24632077750.374092460281.10970912550.294302057923-1.29208372447-0.2551226090460.208370100119-0.457174894721-0.0699852882001-0.1749204229821.249736733110.3983028532790.02238547532760.8339107197040.08121848604940.73364578843199.66131336088.37487989923-45.9757807316
65.403152576580.24007691806-1.430884236280.02348381921110.3113040740674.303526399430.34718982078-0.5085034062210.5043993110280.03086222075180.2666834846110.211010373215-0.358519985310.46644148235-0.5734932887150.9095873632440.147571140205-0.0921530759480.512812728628-0.0914954633960.706401408512106.3268129526.23977620763-22.2657055646
72.95126704955-0.2926042631540.173079941772.82103784886-0.9277184341910.200446977570.007399797361270.136993214407-0.508557802692-0.032825288985-0.256913324065-0.323720680176-0.155286151130.0915034834830.1988264058521.05516979350.333555380481-0.1017930105160.796822440603-0.02315565516251.03915419464126.830432069-16.4383279078-27.9988901081
86.507853142322.611422049970.1930568359011.67583912539-1.568096520652.8276869046-0.2205935085630.508097185932-0.764709653602-0.277529428050.08868041011-0.2719739347330.3286294820980.3412116311390.1680911225741.005245324050.340076872269-0.05439246549790.782434323049-0.1163089107210.9446441884131.40161851-15.736146923-35.0128446787
95.280483623790.851903326612-1.398310712382.998774459931.71424721373.90038542429-0.2413447684810.106552090858-0.202435904682-0.120423954337-0.488811464897-0.680443079616-0.409573623626-0.3876681774720.5664632969641.049055926960.182280515475-0.02660580453560.630397599217-0.1294766100980.943854639121113.944520745-22.7767319704-34.9475189191
104.009281172640.22302892812-0.1768256070663.37361757419-0.1261394182684.20952390192-0.00801930840832-0.233956279973-0.5169710031880.200411812682-0.2940912416450.380686694644-0.335183209462-0.6641827954790.2958902595790.987423571880.232185251108-0.01208785874940.698938413303-0.1773662186870.932246416734105.811128937-24.3976774906-33.7222646908
114.229817784710.6448276245051.977667932993.14130808976-0.7883558048136.26617892250.2214882110420.00847146498035-0.463900323202-0.54737946208-0.383719222769-0.1833602904940.384281168671-0.3239387419650.2040903338690.9668339709850.2417474934520.02256752421110.599457151637-0.1024825108750.840281125669110.371818964-24.8606227684-33.6744192983
125.05107966772-0.06655885901142.078048476062.762532310750.2654782354255.49017860474-0.1324075760210.258831885517-0.73220649228-0.1936195061470.433086987238-0.108280343599-0.06216369011580.431007370231-0.2918779966961.33466247520.3502634087640.05564464053160.707899534541-0.1015728293630.981281430397112.997116365-29.0843984283-40.8519734202
132.555656430510.50363740339-0.9012135203954.917800598321.830689069911.1895906075-1.830512534880.08951789106880.358389450905-0.53170964315-0.1612380973730.796989600618-1.5423468379-0.4245695898431.993179455871.198496908530.264559525616-0.2157971434780.966820383165-0.0961950296040.78481233461593.54429916414.428442803-36.044092086
143.70484488432.298333920760.5483370739412.072015175550.549157022934.940976590970.30025041033-0.650661200211-0.8503693937281.58291507958-0.0248942702823-0.8350749835840.275853437335-0.437880356747-0.1823621510221.05101312930.100384622622-0.07383039788080.7899884289440.2227598965451.0662483571943.083836603-30.570215401-19.9681216376
156.035814653783.110111720970.9929678557485.08221826039-1.493890776884.07915856330.03545524458410.0549845829575-0.4570922643090.05543799008590.01738140526140.1739462874240.0587262956788-0.207717345508-0.04148902888580.7705871597650.1961042738350.04431483954670.555830732290.04429473297460.62086849644740.9080615744-23.9181403457-28.1369305
160.912032701323-0.334305552040.4903551664980.0278336747025-0.1207738940122.30963035698-0.10321612361-0.227995533778-0.8123980849050.863513270312-0.392756622785-0.09690899463890.850939874104-0.2767907785380.3289373298611.236753663720.07883980053740.1021818213750.8099481032230.156505378531.4144073789151.7543418831-44.221123487-22.6849251234
173.825918881191.55261282427-0.08988966701355.013049783580.8474241508737.794302216850.0161617353651-0.179178688412-0.5812881381460.991212029660.186399344746-0.2459602558750.6423824729921.53965736122-0.3023733820531.319866423380.3322642103820.01832849464521.387117620670.1629911594361.1256496412269.4750852241-47.705178522-16.00658104
184.785087840271.46727705476-0.286596226246.412701982210.1839662772665.95742249528-0.707605874793-0.00708925721796-0.277212176594-0.1458105721770.2730133664780.2422317960951.220682892120.4522472525760.6088708810651.410257138650.155188489589-0.02536851990960.8195757084230.1788546936821.1905667646962.1034962904-45.6117130637-25.2078605629
193.330227845721.312619151130.909125589954.856631426290.07693082506474.770974794760.214658978948-1.81432832511-0.8198233787490.9632104401130.0452046551221-0.09813742167030.851402366285-0.871636741655-0.1327874482081.779831070440.243774110143-0.01667021929631.593634512620.3442181873891.2591730704967.0183036386-50.7762893435-13.2364378317
205.663989434070.8142581707584.376314905524.14517171712-0.8506499187326.20187350150.4677203441610.1390129269350.478547800771-0.569229143333-0.204651890763-0.492995214885-0.1925616795330.261213777748-0.2736542357720.8584876558140.2009612422830.2724594291810.7650747879390.005973911028910.89396942744759.2242508039-8.88969780237-25.9487735488
213.33888115731-2.36827052642-0.03769578214632.621706625430.6202007825513.02531437706-0.295777309092-0.769362161748-0.1008599507290.1379457414860.508007751106-0.0234233564442-0.3056972131920.330895698241-0.1083230470150.791955147250.2194546006050.1665934227630.8065224103450.0009797627991280.80605767390163.4748361347-17.0775724862-24.6574878773
222.263427095163.057208454070.7597060236544.539866808441.834762865973.28650842474-0.0704691884314-0.344439913686-0.3282565747560.3586819887030.295059361485-0.2688539709770.41768696660.341524575052-0.1652169088360.8693407893620.341978144442-0.07646526967880.998239828398-0.01618834739250.88606217663174.6700399117-38.2377163473-26.6643616419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 162 )
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 174 )
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 197 )
8X-RAY DIFFRACTION8chain 'A' and (resid 198 through 275 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 20 )
10X-RAY DIFFRACTION10chain 'B' and (resid 21 through 57 )
11X-RAY DIFFRACTION11chain 'B' and (resid 58 through 84 )
12X-RAY DIFFRACTION12chain 'B' and (resid 85 through 100 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 9 )
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 24 )
15X-RAY DIFFRACTION15chain 'D' and (resid 25 through 102 )
16X-RAY DIFFRACTION16chain 'D' and (resid 103 through 119 )
17X-RAY DIFFRACTION17chain 'D' and (resid 120 through 153 )
18X-RAY DIFFRACTION18chain 'D' and (resid 154 through 168 )
19X-RAY DIFFRACTION19chain 'D' and (resid 169 through 202 )
20X-RAY DIFFRACTION20chain 'E' and (resid 2 through 93 )
21X-RAY DIFFRACTION21chain 'E' and (resid 94 through 120 )
22X-RAY DIFFRACTION22chain 'E' and (resid 121 through 241 )

+
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://pdbjlvh1.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