[English] 日本語
Yorodumi
- PDB-8trq: T cell recognition of citrullinated vimentin peptide presented by... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8trq
TitleT cell recognition of citrullinated vimentin peptide presented by HLA-DR4
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • A07 TCR alpha chain
  • A07 TCR beta chain
  • Vimentin
KeywordsIMMUNE SYSTEM / immune receptor complex
Function / homology
Function and homology information


keratin filament binding / lens fiber cell development / regulation of interleukin-4 production / intermediate filament organization / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / cellular response to muramyl dipeptide ...keratin filament binding / lens fiber cell development / regulation of interleukin-4 production / intermediate filament organization / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / cellular response to muramyl dipeptide / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / structural constituent of eye lens / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / astrocyte development / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / intermediate filament cytoskeleton / CD4 receptor binding / Striated Muscle Contraction / intermediate filament / RHOBTB1 GTPase cycle / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / cell leading edge / Bergmann glial cell differentiation / polysaccharide binding / negative regulation of type II interferon production / microtubule organizing center / humoral immune response / positive regulation of collagen biosynthetic process / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / Caspase-mediated cleavage of cytoskeletal proteins / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / phagocytic vesicle / regulation of mRNA stability / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / Late endosomal microautophagy / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / cellular response to type II interferon / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / cognition / nuclear matrix / positive regulation of protein phosphorylation / Chaperone Mediated Autophagy / Interferon gamma signaling / neuron projection development / Aggrephagy / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / peroxisome / Downstream TCR signaling / T cell receptor signaling pathway / double-stranded RNA binding / negative regulation of neuron projection development / cellular response to lipopolysaccharide / scaffold protein binding / early endosome membrane / Interleukin-4 and Interleukin-13 signaling / molecular adaptor activity / adaptive immune response / positive regulation of viral entry into host cell / cytoskeleton / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / immune response / Golgi membrane / protein domain specific binding / axon / lysosomal membrane / external side of plasma membrane / focal adhesion
Similarity search - Function
Intermediate filament head, DNA-binding domain / : / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / MHC class II, beta chain, N-terminal ...Intermediate filament head, DNA-binding domain / : / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / 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
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Vimentin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLoh, T.J. / Lim, J.J. / Reid, H.H. / Rossjohn, J.
Funding support Australia, United States, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2008981 Australia
Janssen Pharmaceuticals United States
CitationJournal: Nat Commun / Year: 2024
Title: The molecular basis underlying T cell specificity towards citrullinated epitopes presented by HLA-DR4.
Authors: Loh, T.J. / Lim, J.J. / Jones, C.M. / Dao, H.T. / Tran, M.T. / Baker, D.G. / La Gruta, N.L. / Reid, H.H. / Rossjohn, J.
History
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 30, 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: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1 beta chain
C: Vimentin
D: A07 TCR alpha chain
E: A07 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,54916
Polymers97,2045
Non-polymers1,34511
Water66737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.603, 76.616, 224.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

-
HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21919.594 Da / Num. of mol.: 1 / Fragment: UNP residues 30-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Homo sapiens (human) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1 beta chain / Human leukocyte antigen DRB1 / HLA-DRB1


Mass: 23206.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: P01911

-
Protein , 2 types, 2 molecules DE

#4: Protein A07 TCR alpha chain


Mass: 22991.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein A07 TCR beta chain


Mass: 27647.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria)

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

#3: Protein/peptide Vimentin


Mass: 1438.634 Da / Num. of mol.: 1
Fragment: UNP residues 59-71 with modified residue citrulline (CIR) at position 64
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08670
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

-
Non-polymers , 2 types, 47 molecules

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


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.77 % / Description: Plate-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% w/v PEG3350, 0.2 M di-sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, tri-glycine additive

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.75→46.55 Å / Num. obs: 27166 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 66.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.157 / Net I/σ(I): 12.4
Reflection shellResolution: 2.75→2.9 Å / Rmerge(I) obs: 1.767 / Num. unique obs: 3877 / CC1/2: 0.732

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6V1A

6v1a


Resolution: 2.75→46.55 Å / SU ML: 0.3681 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9679
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2637 1315 4.85 %
Rwork0.216 25783 -
obs0.2183 27098 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.21 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6513 0 88 37 6638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00896757
X-RAY DIFFRACTIONf_angle_d1.0179191
X-RAY DIFFRACTIONf_chiral_restr0.05571012
X-RAY DIFFRACTIONf_plane_restr0.00931191
X-RAY DIFFRACTIONf_dihedral_angle_d13.66162372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.860.37061480.30872797X-RAY DIFFRACTION100
2.86-2.990.33271520.29042796X-RAY DIFFRACTION99.97
2.99-3.150.31461360.26772824X-RAY DIFFRACTION99.93
3.15-3.350.2911350.25712861X-RAY DIFFRACTION99.9
3.35-3.60.27471520.22182800X-RAY DIFFRACTION99.9
3.6-3.970.27961640.222838X-RAY DIFFRACTION100
3.97-4.540.21531330.18562907X-RAY DIFFRACTION99.97
4.54-5.720.23621430.18362889X-RAY DIFFRACTION99.97
5.72-46.550.25521520.20853071X-RAY DIFFRACTION99.81
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)
16.994516729417.07834643776-1.953697700142.20469690343-0.1200033784384.296875010330.491900163059-1.285808122470.4555535458050.0693068926645-0.761537508590.2842398066690.3056316954730.8068201897940.1312195014240.8887066478720.08288951339080.1546809505040.7259274936670.01789199802670.5426738930086.43259008228-5.6168085683763.3000465639
21.83249023053-0.9719387833922.323951187182.316861560663.566410567012.028219182840.322362720449-0.175435568409-0.2937479056850.05708578435780.40407717056-0.1367408289451.45686290999-0.71066059286-0.6276226346740.534246847358-0.0457828491023-0.006206690328720.3708855794710.02768686365080.393330588418-1.7180347326-6.0381756708948.5337302452
310.4431028707-1.54377395321-8.348966788116.276822300073.360237001522.720951201060.77220800126-1.151513291460.4093897559930.435568490450.0332702489277-0.013622375074-1.525402062611.45430145777-0.9449670833430.796135248339-0.106550205187-0.03356896174460.583144011678-0.05898319375210.4668632922284.477538850774.2653017193259.2177113446
45.090814166815.244153563380.6054496803532.140935080313.208431151924.21703422680.7045385642460.305501977775-0.02151530095972.00926245247-0.6555714679750.8469396718750.541110807713-0.046020227287-0.05065963378150.831667054218-0.07265535229160.01116222834640.600730884433-0.06586238810730.3477269286583.82400891489-20.936546242715.3793359998
54.16939934080.269613463308-3.787723298681.999826878360.3619723020418.432484254190.4858532742190.05191799913340.457025254663-0.0693616962326-0.015416722147-0.176718929289-0.7518582672290.525180216729-0.4367231396080.750725524885-0.01459151738940.04157775537320.467772517627-0.01254978073990.36558644120520.1537682054-15.5906505051-1.89362675603
63.731319486170.696337094356-5.749265583930.9308028697590.2014109604662.260010332040.0752004740815-0.224259936765-0.540745277143-0.403101656939-0.445567153853-0.289823989886-0.1135241591160.162952768385-0.2857776201660.9880171507030.1293411251390.1639048227391.091096993020.009839651729280.51866244755434.9624193571-18.9318009343-21.7589232808
79.443636444383.666325093930.3630427112773.87629716002-2.607207646396.753285748160.09456626872650.271457701684-0.1585971646910.03558354561450.15514305034-0.1682732954710.02784052667360.0790353865587-0.1555420016630.7083356453840.07630180091510.03509196987930.43064243264-0.01383850868790.50543378046631.2702361575-17.8931838672-37.6008690732
80.3841826805810.625421107611.146867274621.25773586911.568875818248.220643028870.181597270431-0.2834125282630.1982287636160.2858299624410.1058531520430.1258020092660.127733558766-0.790481585345-0.1464975150750.6784250866880.03828611515420.05544308841790.5871831670810.01442651531210.4237048519430.333187814985-21.4588126409-13.1853055132
97.74710441786-1.91803547570.7151714902653.59133478905-0.6762644970660.946418195960.101363467091-0.145429755802-0.2552635161150.06565944624230.00248882249273-0.126083941251-0.004514274182970.0282147047497-0.09419824853230.6711410701560.0844730235444-0.08438284812580.428023809451-0.02978607715250.3210479690818.3007062225-27.9140040018-36.9062436458
105.616615137632.35751749042.304225152916.56161304095.359682216096.639919817740.2886051495690.1727496132750.0656793464043-0.134989834721-0.1589875081880.100252801099-0.0462843495998-0.630574047353-0.1798712166050.660167704453-0.05064325167330.08557157881910.4961699200080.0158138349950.351967126743-1.90979316159-10.746905843423.4187124543
113.98079511551-0.136894953553-0.6070555159687.113244207075.80373851037.58589873182-0.2452610548160.66242326687-0.444156386508-0.09156913778420.1691578978380.8073539956730.856707566265-0.7762314751330.07680823862630.738220665985-0.153613896059-0.03301799548730.556343452011-0.01509044656430.547903494762-8.38572224705-28.173569814319.9624113353
126.35009771016-3.38226140686-2.468998486992.000338495837.937835641597.970861786470.225757741302-0.01142810396410.5417375200390.679324085232-0.00572153243032-0.07960376296160.0741808700887-0.0966700937214-0.3141177892010.608846434271-0.01062185105940.02337843910880.5635693906480.01728851702910.425617993258-12.5550539245-1.5135022159846.3741674782
136.8002711624-3.42714859832-5.118973927644.908080003734.942933060885.20027847185-0.3306467758490.46786239973-0.207910019540.497655465796-0.2766710688670.4772808441930.445223861728-0.6707546395130.4893215011680.682069916183-0.1178858082960.01225463621150.524780761336-0.006479014391440.334511874836-14.7703466273-10.944058092735.2492649154
146.19839753862-3.95704199256-2.452108159979.652221135146.866530158956.60273061977-0.429208858605-0.310452380341-0.4910129106250.0111402695275-0.2134911102851.07896798859-0.108559463724-0.941995198560.4478937231530.6818392344770.0239229558850.05233998451660.6939191650390.07841927032630.438740723363-18.2767622102-5.2370808962239.906665633
156.222108875061.984837587062.996888785422.646060394373.655980900766.74985843167-1.52716561872-0.0943540224173-0.02819622934171.34590388339-0.04162382766022.995440205910.825517286074-1.674400417051.394880152390.860948814026-0.3937182365160.4746777158250.849844832491-0.05863217154870.601869196032-21.5292416793-13.365204246143.4767353518
162.733460754792.565600391211.422390630746.140697342122.898939334034.39298760529-0.0438526702958-0.356711675855-0.5893096995410.4340244388490.126467602537-0.1420569434510.806171783215-0.14677350527-0.01936598303330.899422137174-0.02966886664710.1146913833410.3841571148970.01234477666970.4061650512552.77313583151-23.117094714426.1818134285
179.359434250174.27088864871-4.78553794926.7798895176-1.73519203765.2935438427-0.2009376208680.0746268653155-1.147638024720.523497713681-0.3525598180950.1066141584750.887255439432-0.3526751779470.5334347856241.24276046951-0.06326736347110.1798681519960.483190346244-0.04666780666250.5882400487326.61427249618-31.619590746625.4205775553
181.610896356-2.25088882603-3.383184552215.2274490353.949499150679.000952164550.050539764262-0.0486302821022-0.190575792478-1.48862759407-0.110758141920.0451534326521-0.4418488925720.157043975114-0.03214880100630.558767493158-0.0328626995678-0.0795863920540.4084861993480.05671799614720.45295758668710.3616044429-18.452010877621.9652825545
195.28258023472.17517822886-6.525750073824.87769343194-5.24504419162.328144947830.4968024188330.03814807460230.2213235895040.02851410638090.1199828343390.440287621478-0.876361436175-0.465843265191-0.7702357473840.638981575623-0.03468870698390.03766351917670.333719630461-0.01071354335870.490291566104-5.295478406610.10581345054559.9699187852
208.638775746761.61411085779.24858009927.605000555074.92274990492.04487726028-0.7687189937420.389747274290.1708120834110.20424456425-0.130701314949-0.2520582308870.2924169348751.744710820190.4010917523890.702800629257-0.05411983161790.1584830898820.4027173228510.01569257375070.3399597570046.95037451866-3.2088864840252.7616612963
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 134 through 144 )BE134 - 144132 - 142
22chain 'B' and (resid 145 through 164 )BE145 - 164143 - 162
33chain 'B' and (resid 165 through 192 )BE165 - 192163 - 190
44chain 'C' and (resid 59 through 71 )CF59 - 711 - 13
55chain 'D' and (resid 1 through 120 )DG1 - 1201 - 108
66chain 'D' and (resid 121 through 134 )DG121 - 134109 - 122
77chain 'D' and (resid 135 through 218 )DG135 - 218123 - 205
88chain 'E' and (resid 1 through 136 )EH1 - 1361 - 123
99chain 'E' and (resid 137 through 256 )EH137 - 256124 - 243
1010chain 'A' and (resid 3 through 55 )AA3 - 551 - 53
1111chain 'A' and (resid 56 through 87 )AA56 - 8754 - 85
1212chain 'A' and (resid 88 through 101 )AA88 - 10186 - 99
1313chain 'A' and (resid 102 through 144 )AA102 - 144100 - 142
1414chain 'A' and (resid 145 through 166 )AA145 - 166143 - 164
1515chain 'A' and (resid 167 through 182 )AA167 - 182165 - 180
1616chain 'B' and (resid 3 through 32 )BE3 - 321 - 30
1717chain 'B' and (resid 33 through 51 )BE33 - 5131 - 49
1818chain 'B' and (resid 52 through 97 )BE52 - 9750 - 95
1919chain 'B' and (resid 98 through 122 )BE98 - 12296 - 120
2020chain 'B' and (resid 123 through 133 )BE123 - 133121 - 131

+
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