[English] 日本語
Yorodumi
- PDB-7qng: Structure of a MHC I-Tapasin-ERp57 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qng
TitleStructure of a MHC I-Tapasin-ERp57 complex
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Protein disulfide-isomerase A3
  • Tapasin
KeywordsIMMUNE SYSTEM / MHC I / chaperone complex / endoplasmic reticulum / peptide editing
Function / homology
Function and homology information


MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / Calnexin/calreticulin cycle / MHC class I protein complex binding / TAP2 binding / TAP1 binding / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity ...MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / Calnexin/calreticulin cycle / MHC class I protein complex binding / TAP2 binding / TAP1 binding / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / regulation of protein complex stability / phospholipase C activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / cellular response to interleukin-7 / positive regulation of extrinsic apoptotic signaling pathway / TAP complex binding / protein disulfide isomerase activity / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protein-disulfide reductase activity / phagocytic vesicle / extrinsic apoptotic signaling pathway / protein folding chaperone / endoplasmic reticulum-Golgi intermediate compartment membrane / response to endoplasmic reticulum stress / 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 / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / MHC class II protein complex / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / platelet aggregation / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / unfolded protein binding / melanosome / protein folding / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / regulation of gene expression / protein-containing complex assembly / molecular adaptor activity / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / cysteine-type endopeptidase activity / focal adhesion
Similarity search - Function
Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Tapasin / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / : / Thioredoxin domain profile. ...Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Tapasin / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / : / Thioredoxin domain profile. / Thioredoxin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Thioredoxin-like superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tapasin / H-2 class I histocompatibility antigen, D-B alpha chain / Protein disulfide-isomerase A3 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMueller, I.K. / Thomas, C. / Trowitzsch, S. / Tampe, R.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)TA157/12-1 Germany
European Research Council (ERC)789121European Union
CitationJournal: Nat Commun / Year: 2022
Title: Structure of an MHC I-tapasin-ERp57 editing complex defines chaperone promiscuity.
Authors: Muller, I.K. / Winter, C. / Thomas, C. / Spaapen, R.M. / Trowitzsch, S. / Tampe, R.
History
DepositionDec 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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: Tapasin
B: Protein disulfide-isomerase A3
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,3975
Polymers145,8104
Non-polymers5871
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-20 kcal/mol
Surface area58080 Å2
Unit cell
Length a, b, c (Å)74.760, 168.530, 187.050
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

-
Protein , 4 types, 4 molecules ABCD

#1: Protein Tapasin / TPN / TPSN / NGS-17 / TAP-associated protein / TAP-binding protein


Mass: 44881.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAPBP, NGS17, TAPA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15533
#2: Protein Protein disulfide-isomerase A3 / 58 kDa glucose-regulated protein / 58 kDa microsomal protein / p58 / Disulfide isomerase ER-60 / ...58 kDa glucose-regulated protein / 58 kDa microsomal protein / p58 / Disulfide isomerase ER-60 / Endoplasmic reticulum resident protein 57 / ER protein 57 / ERp57 / Endoplasmic reticulum resident protein 60 / ER protein 60 / ERp60


Mass: 56830.199 Da / Num. of mol.: 1 / Mutation: C60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDIA3, ERP57, ERP60, GRP58 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30101, protein disulfide-isomerase
#3: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32218.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#4: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

-
Sugars / Non-polymers , 2 types, 53 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 4.04 Å3/Da / Density % sol: 69.59 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM Gly-Gly, AMPD, pH 8.5, 300 mM lithium sulfate, 300 mM sodium sulfate, 300 mM potassium sulfate, 20% (v/v) PEG8000, 40% (v/v) 1,5-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→48 Å / Num. obs: 65719 / % possible obs: 99.76 % / Redundancy: 5.9 % / Biso Wilson estimate: 87.61 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.9
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 6491 / CC1/2: 0.443

-
Processing

Software
NameVersionClassification
PDB-REDOrefinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ENY

6eny


Resolution: 2.7→48 Å / SU ML: 0.4301 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 3284 5 %
Rwork0.1983 62368 -
obs0.1999 65719 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.17 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9621 0 48 52 9721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00949942
X-RAY DIFFRACTIONf_angle_d1.356513507
X-RAY DIFFRACTIONf_chiral_restr0.08151425
X-RAY DIFFRACTIONf_plane_restr0.00491774
X-RAY DIFFRACTIONf_dihedral_angle_d12.31713698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.36851400.3332673X-RAY DIFFRACTION99.86
2.74-2.780.32891420.31952696X-RAY DIFFRACTION99.79
2.78-2.830.32891410.31242662X-RAY DIFFRACTION100
2.83-2.880.48541420.42062709X-RAY DIFFRACTION99.96
2.88-2.930.43421400.40932655X-RAY DIFFRACTION99.96
2.93-2.990.38061420.34732699X-RAY DIFFRACTION99.93
2.99-3.050.3241390.29662646X-RAY DIFFRACTION99.89
3.05-3.110.29751440.26522721X-RAY DIFFRACTION99.79
3.11-3.190.30621400.25062670X-RAY DIFFRACTION100
3.19-3.270.28091420.23512697X-RAY DIFFRACTION99.82
3.27-3.350.29531420.23692681X-RAY DIFFRACTION99.89
3.35-3.450.29121400.26382678X-RAY DIFFRACTION99.65
3.45-3.560.27311430.25112716X-RAY DIFFRACTION99.9
3.56-3.690.28191420.20882693X-RAY DIFFRACTION99.93
3.69-3.840.23341410.19032695X-RAY DIFFRACTION99.75
3.84-4.010.20261430.18932716X-RAY DIFFRACTION99.79
4.01-4.220.20761430.18112704X-RAY DIFFRACTION99.93
4.23-4.490.18691430.15892725X-RAY DIFFRACTION99.83
4.49-4.840.17381450.14342734X-RAY DIFFRACTION99.9
4.84-5.320.17871450.15362760X-RAY DIFFRACTION99.83
5.32-6.090.20031450.17652751X-RAY DIFFRACTION99.76
6.09-7.670.20891470.19082797X-RAY DIFFRACTION99.56
7.67-480.20231530.16742890X-RAY DIFFRACTION98.42
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)
12.09891198150.6139797495460.3657597657547.33771276860.4972921724412.92376667952-0.0405762598555-0.1538401292690.08608880077970.348167541171-0.154469485806-0.505790321279-0.2959531832350.2706213693830.2237680246580.457320040189-0.0230114989151-0.07348625316620.6076255595550.07481744926510.5846380049641.23443008571.547090390732.8117343186
25.44674111821-0.6465718507953.163342975143.3701987374-0.5481408165645.701063811470.110143605938-0.0467723093304-0.1640969926650.140343427021-0.0827971288741-0.2449088705250.2233866071170.235103080211-0.02718947262390.400132573267-0.001738388149690.07329669628680.3931084474370.03820498947950.45884148011534.397924122854.085386262223.4211643095
37.53456325566-2.06034147781.136869629257.09618753112-3.182805799427.24347370265-0.1085062807920.7851911493410.434225959908-0.7726552269580.2096397624380.586835288493-0.295701556293-0.555584523277-0.107158014240.606479757996-0.0485144855341-0.08197367454340.6475186142340.01212694087030.5506759637265.5979509998670.4681383787-6.25705231943
44.72327063975.98148198517-4.520326599261.99995415368-3.475765986485.621636046020.347914966331-0.257482238279-0.159537184514-1.50173432874-1.21325944486-5.734042785521.35403517761-0.1103538452320.8377593969252.707869747650.5805213726230.07082804812371.696159079980.03167314322322.334313875153.5265655309861.4599316799-21.5864070561
54.481069418760.65450752668-1.031543826017.36893130782-3.242095017733.39889671486-0.137227065748-0.7248003678830.1170599082751.99201610852-0.0133123487917-0.218717448125-0.8155806935090.1709959261420.1409569092281.514921921350.176611044327-0.1505614488080.9335119409970.1004174458640.66741345224941.877194935654.463370762263.2779037225
60.8778459322040.7788008932421.44249560412.597789441692.231369594456.0791190639-0.09097496227010.1205214329250.105380093114-0.723717314027-0.1191078657470.481067713254-0.735319913510.02180986787410.2359903738540.9892630470090.143715885996-0.1951200764110.5977261091120.04080817344150.70711397971541.282401812721.411244675162.3354016758
72.592877134170.4709774130750.8960476881563.78018725434-1.401333616781.748157303440.7604372971730.673734866615-0.89934696869-0.728879824518-0.353947938911-1.238085350742.109327569351.2695516373-0.3123684297451.63254981610.588507369578-0.1529390896991.11617825836-0.1277170829341.1453733597443.808608411129.123217754916.5005260206
87.560603903711.951723666510.58513861155.87957105682-0.7269265827483.141279641230.188610961441-0.8687350224480.2277830700920.784503600878-0.09240254594090.914805589897-0.325874187376-0.703361651282-0.1155155782950.6297644159030.1363553086190.1390361440540.881656318887-0.0460848627570.6841268767812.3187371514366.945289383236.9536203299
96.84650425319-0.1823907112850.06422293961728.40215645785-1.994308260754.88558147362-0.027413840229-0.347219086985-0.6925155814490.2053345065070.02624215107070.1058767318320.13015582952-0.06864013407750.02739668402960.4690357005440.02914816235610.05560560729790.6416698366410.02362856845320.576375155918.329388933958.596385856134.6925568971
105.042487926641.12710904933-0.04015138227991.13712283835-1.04590623434.837013840470.495822877765-1.1483167091-1.340243883370.1864175340340.009860003395160.3404687542410.637857268276-1.17722352735-0.4362491907920.8345565088690.0372619131396-0.03894479525990.7237594904620.1682720511261.33326252646-1.3731697309149.832069025229.2334814876
117.33992458619-0.6178203908420.7726260135153.56326298214-0.2712158536487.492612496240.3866836647940.824256740212-1.17519850964-0.544527260611-0.07474252997240.5653646757391.25909428905-0.417432416985-0.2938715167070.824109981815-0.219531087478-0.1756906376420.828367735849-0.1082443868820.969299306712-3.3126424878946.92154792494.62243383732
125.26264892882-0.1738889236755.204155662723.77898417824-0.8853711163365.28403719631-1.053535360270.876982065044-0.427126252623-0.7806453466870.529951958927-0.0533563572566-0.5469033337230.09087158518050.5185518486880.519151665663-0.01187433823020.01207364667060.7700253103640.209498608970.79508804222511.208345671570.300082551217.922813288
136.96296938192-4.073441428565.768988346755.62903048626-0.9942068614119.38232136206-0.000452856647550.0814290517838-1.63692947356-0.088521777380.3880128192350.8325326171780.353217520707-0.965712985917-0.3191246026080.634645879502-0.06769879864780.06010577253680.7937943333750.07294262879560.781779766964-4.7171947429863.569542007110.7895801591
144.7817933649-3.438070172021.654385461953.827703583710.6335585853483.02159559581.1213216429-0.000905801040848-0.90144247736-0.633771272930.7342273999082.437418588650.689002923901-1.60966240217-1.834554327110.823019159186-0.226380854515-0.1421164583541.265647509760.1123200815091.55947032275-19.912943078358.99766878697.85169831987
150.0936584370245-0.4788895683330.2140421186823.301011854660.4719960776942.931487031290.515646295795-0.46363462880.325460569915-0.261926869535-0.2571435931880.9227330371850.320980211434-1.30026713302-0.2032145875260.45974556983-0.131034078652-0.04474473434331.135995484580.1609133713110.927106262046-8.0539142374164.973628495714.8220917214
162.00932068728-1.97506757991.985290657574.99943605348-1.678710929882.03410186195-0.432137379423-0.1964867953131.13361505864-0.2220337076010.116744161105-0.0022118201191-0.932732056017-0.4933679276810.2967408722170.6856835195460.1188719593150.03522813921110.8728003099740.1326740967060.851426524667-2.8893959311274.58294901516.4451562008
179.23388352735-2.450701531854.621588829884.82401264616-3.006646183697.80268436421-0.4008981903170.48266166594-0.03057477507890.7177328780250.3275129185271.18279133473-1.25778155259-2.039368802230.03609185548510.5957714886840.1990580201280.1016373507691.048901557990.1407188070091.24275137587-14.250435551276.007746993114.2253830292
183.24241391109-2.581987740293.398814659672.83653123248-0.5606524130559.42947044587-1.00826370143-1.112726908211.264274680241.400198161731.1604024850.404346014244-0.119291221193-0.881275364491-0.1143358793380.7951740908610.04120491243380.07875807684270.6721766656080.001936488046961.09937832073-2.6941612847866.948794892926.6438195984
199.32892438877-2.60826513445.358171536282.27764375939-0.9948756256993.3382796114-0.5258858052010.1370367183990.400062837539-0.01158941638750.2368366174350.743207861212-0.128474134108-0.9645011091720.03220143046080.558210491993-0.03559548835680.03198609898711.08662756430.1311150340441.00829322474-8.2530040338766.350487698414.6467818367
206.734659554067.423444054475.596882899338.139837980696.142480102374.65379667293-0.0941115243685-0.1341553278081.00940416451-0.150647468846-0.17588453650.567952197435-0.411535539127-0.6646735906980.405138850850.5213374342610.115441327295-0.03805944916071.15069455490.1604277895690.906813115317-6.0565383366273.81538839689.7475282462
212.998154552570.6328863097173.520117178374.723001272011.445924138017.52357208294-0.2728654818710.586159309066-0.0219232161656-0.2459887295740.1874015896610.118555945272-0.126011861296-0.3358022401160.1759477192950.453153701740.00529604263633-0.01438819560950.9151852918060.1032605248210.80543620184-2.4565129861470.0211719046.69867966187
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 143 )AA1 - 1431 - 143
22chain 'A' and (resid 144 through 269 )AA144 - 269144 - 269
33chain 'A' and (resid 270 through 380 )AA270 - 380270 - 375
44chain 'A' and (resid 381 through 381 )AB3811
55chain 'B' and (resid 1 through 108 )BF1 - 1081 - 105
66chain 'B' and (resid 109 through 334 )BF109 - 334106 - 331
77chain 'B' and (resid 335 through 467 )BF335 - 467332 - 464
88chain 'C' and (resid 1 through 103 )CG1 - 1031 - 101
99chain 'C' and (resid 104 through 151 )CG104 - 151102 - 149
1010chain 'C' and (resid 152 through 194 )CG152 - 194150 - 192
1111chain 'C' and (resid 195 through 276 )CG195 - 276193 - 274
1212chain 'D' and (resid 0 through 5 )DH0 - 51 - 6
1313chain 'D' and (resid 6 through 11 )DH6 - 117 - 12
1414chain 'D' and (resid 12 through 19 )DH12 - 1913 - 20
1515chain 'D' and (resid 20 through 30 )DH20 - 3021 - 31
1616chain 'D' and (resid 31 through 41 )DH31 - 4132 - 42
1717chain 'D' and (resid 42 through 51 )DH42 - 5143 - 52
1818chain 'D' and (resid 52 through 56 )DH52 - 5653 - 57
1919chain 'D' and (resid 57 through 77 )DH57 - 7758 - 78
2020chain 'D' and (resid 78 through 83 )DH78 - 8379 - 84
2121chain 'D' and (resid 84 through 99 )DH84 - 9985 - 100

+
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