[English] 日本語
Yorodumi
- PDB-7ryo: CD1a-dideoxymycobactin-gdTCR complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ryo
TitleCD1a-dideoxymycobactin-gdTCR complex
Components
  • (T cell receptor ...) x 2
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1a
KeywordsIMMUNE SYSTEM / CD1 / TCR / lipid antigen
Function / homology
Function and homology information


exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / alpha-beta T cell receptor complex / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / immunoglobulin complex ...exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / alpha-beta T cell receptor complex / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / immunoglobulin complex / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / membrane raft / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / : / MHC-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like ...: / : / MHC-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / 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
dideoxymycobactin-838 / T cell receptor gamma variable 4 / T cell receptor delta variable 1 / T cell receptor alpha chain constant / T cell receptor beta constant 1 / T-cell surface glycoprotein CD1a / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWegrecki, M. / Le Nours, J. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Nat Commun / Year: 2022
Title: Atypical sideways recognition of CD1a by autoreactive gamma delta T cell receptors.
Authors: Wegrecki, M. / Ocampo, T.A. / Gunasinghe, S.D. / von Borstel, A. / Tin, S.Y. / Reijneveld, J.F. / Cao, T.P. / Gully, B.S. / Le Nours, J. / Moody, D.B. / Van Rhijn, I. / Rossjohn, J.
History
DepositionAug 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: 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 18, 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 / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-cell surface glycoprotein CD1a
B: Beta-2-microglobulin
C: T cell receptor gamma variable 4,T cell receptor beta constant 1
D: T cell receptor delta variable 1,T cell receptor alpha chain constant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8648
Polymers96,8054
Non-polymers1,0584
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)234.881, 42.239, 124.656
Angle α, β, γ (deg.)90.000, 113.348, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein T-cell surface glycoprotein CD1a / T-cell surface antigen T6/Leu-6 / hTa1 thymocyte antigen


Mass: 32593.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1A / Production host: Homo sapiens (human) / References: UniProt: P06126
#2: Protein Beta-2-microglobulin


Mass: 12602.105 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: Homo sapiens (human) / References: UniProt: P61769

-
T cell receptor ... , 2 types, 2 molecules CD

#3: Protein T cell receptor gamma variable 4,T cell receptor beta constant 1


Mass: 27987.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRGV4, TCRGV4, TRBC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0C4DH28, UniProt: P01850
#4: Protein T cell receptor delta variable 1,T cell receptor alpha chain constant


Mass: 23622.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRDV1, TRAC, TCRA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B0GX56, UniProt: P01848

-
Non-polymers , 3 types, 4 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-WGR / dideoxymycobactin-838 / (2R)-4-oxo-4-{[(3S)-2-oxoazepan-3-yl]amino}butan-2-yl N~2~-[(4S)-2-(2-hydroxyphenyl)-4-methyl-4,5-dihydro-1,3-oxazole-4-carbonyl]-N~6~-[(2Z)-icos-2-enoyl]-L-lysinate


Mass: 838.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H75N5O8 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3→43.86 Å / Num. obs: 23043 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 62.41 Å2 / CC1/2: 0.989 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.18 Å / Num. unique obs: 3638 / CC1/2: 0.703

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RYM

7rym


Resolution: 3→39.96 Å / SU ML: 0.4371 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2593
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2667 1151 5 %
Rwork0.2217 21873 -
obs0.224 23024 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.33 Å2
Refinement stepCycle: LAST / Resolution: 3→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6215 0 73 0 6288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026462
X-RAY DIFFRACTIONf_angle_d0.55998815
X-RAY DIFFRACTIONf_chiral_restr0.0414953
X-RAY DIFFRACTIONf_plane_restr0.0041140
X-RAY DIFFRACTIONf_dihedral_angle_d13.59882242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.140.38851300.33642671X-RAY DIFFRACTION99.29
3.14-3.30.33481520.29072676X-RAY DIFFRACTION99.37
3.3-3.510.34291320.25852758X-RAY DIFFRACTION99.42
3.51-3.780.29491480.24452692X-RAY DIFFRACTION99.51
3.78-4.160.27761410.21482707X-RAY DIFFRACTION99.48
4.16-4.760.22221390.1732751X-RAY DIFFRACTION99.59
4.76-5.990.24611490.1962773X-RAY DIFFRACTION99.93
5.99-39.960.21871600.20762845X-RAY DIFFRACTION99.01
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)
11.44849078781-0.151819865911.228535331412.28578672234-1.051726954564.56032779891-0.07095965013330.108933768078-0.317493581196-0.2248407677140.208283827851-0.1117612737430.335178039013-0.413310654981-0.1494213595320.339942273705-0.004386506025410.1497846092010.348522880314-0.06093795349240.81106626557317.863190712410.0617669431-4.73406035086
20.8325850104741.40007234583-0.09593027850522.691154000620.06075176040160.95645034566-0.03462837491620.0956815082884-0.00266168327008-0.0414792882682-0.0166491715971-0.3130582573810.0562103278272-0.157721143611-0.09937995720320.379173743544-0.07243243778570.214348608976-0.04101041567250.05612724399471.0848181604151.814155503828.0910203857-1.04652187998
37.909307136221.0400104304-3.329712533252.051068335891.632305726813.64107272609-0.199697970361-0.739201697452-2.002653411450.0589341568723-1.165226093330.3099725851281.83078659132-0.1027663809131.345896262240.687600444841-0.05248331095480.08719241524570.5148521008740.2155568632771.2448235895532.8670344817.2562984377412.8047088064
43.34511185582-1.90477342033-0.8432092285834.388762066030.05601331308064.205423985640.00256853471966-0.3569162974430.57768486724-0.4385941058210.151932089778-1.03795079156-0.3074965140170.265523792138-0.1808726986020.4141223047470.101731344559-0.04134237906710.23076922382-0.008378994534640.78287345229141.807691169732.50300418357.98672692155
53.21906362064-1.075133392040.1814518476711.29586103568-0.6524332315822.53496709971-0.0308334060251-0.365020380692-0.2384360795080.2428412041390.395354098845-0.234716790353-0.10557960967-0.21215940062-0.2956584791840.117199032047-0.0313469821193-0.01013409030830.333457921133-0.07331393551160.45765678369835.597725889726.38652969578.1439857018
66.245364900761.37240203623-1.50904021894.482408923540.3491904975390.475827455230.0405350930269-0.592133370614-0.2693078919210.06923015178220.489733085197-0.0716731253980.477434261525-0.187828033411-0.5763735978680.6227851697280.0887027797495-0.1745140152260.3133049488440.1546587481290.64175139913326.762042109214.540374569113.7659450243
74.146238327513.287857635330.8827766013154.43392278464-2.212674453015.331375249380.197197870131-1.54610880090.7208848882240.412803309966-0.2568816180811.16720398794-0.195528936185-0.2162367852950.02082261847770.356010564253-0.05823684514590.07242033592640.523002191348-0.1430657616960.76358733574532.752741750231.087636683519.9248178293
83.357237404563.238295271783.403278524897.826013579417.57898238137.45775099877-0.2395056590780.105564223020.135562494727-0.739845946346-0.1564224357011.3631885136-0.925403196763-0.5248469042110.5209783557820.4477524228980.00815411784236-0.01276938943030.3275977524190.07362751183740.7380624141426.101682351324.96910209017.40931409067
93.86586731023.335501381212.060829518413.434471415243.03875954754.32250685840.05214935552240.1328678098080.366766424779-0.1723356853150.536788259163-0.4504434192590.2202378509750.196650438257-0.5864771637850.3099537639530.1000298179710.09836055115080.2939619411450.06333409245050.64749550742131.732894769422.06850257185.87001220796
103.15676350501-1.832482631660.02642453927921.68914127366-0.5577576957744.070471569220.611987424053-0.1894603371870.7638747709930.871884738069-0.373110272792-1.39870018603-0.8220630643820.521502695212-0.08769205039410.678907197037-0.02415716754820.07870193642480.23335032620.05382076078980.76917261530439.719456401733.523219059518.5572170652
117.560562430973.14139920423-5.740483514883.32070595578-0.2019406392677.307671615220.0172213027844-1.31872459375-1.670809214791.01770244327-0.449017187061-1.098237334160.8248398997680.1149085800420.4465338085660.536825159364-0.01357052317290.1098800343160.5512059282150.2674657818080.73378595662932.889570161214.194076173521.147752262
125.374260903255.25289287564-4.333465149065.20834922206-3.714172469737.23671732472-0.0828391787886-0.804900951973-0.229588068850.3659809740160.112127292479-1.79402785167-0.05670662732790.760868596839-0.04418236801340.4351239774970.031307368978-0.05055205762080.4272827295020.0168856715120.84183858547144.112549088528.493021387616.1587934435
131.886043897930.937345997591-0.6525666392832.29486252517-0.9616368374164.08172358845-0.101296552853-0.00676711342435-0.100244207838-0.05538822251560.09175379149670.1801981850240.138585928217-0.1958908769340.05646201746360.4358351507450.009287137377670.1340971760150.5757020561470.04223089392960.600737723371-1.688892039793.7856312115424.9298932313
141.846298051660.61589998962-0.9154883456581.63147575046-0.4292166665963.34793652449-0.0695841289866-0.35663585224-0.0848763707070.2642346939980.003041128400110.2112285715440.0693937336934-0.34157876988-0.0007623209116630.39319445150.0313272938710.1520421844580.5871590774490.1223371880870.676443396967-3.271220260154.5335127224436.6446359958
152.155509658780.1743799788090.424412894114.771014910782.844015741485.73888879220.220438348353-0.6135888568110.02756766883260.93993749331-0.03113101768360.0887608470257-0.2878179832910.287124223524-0.1600384708091.11645345692-0.1366515152310.04366145693161.034516877270.3528290719590.673825071518-9.919311366351.18676113963.7226761751
162.389977983460.9444461154450.6207443491442.88682660995-2.157963364832.48846754691-0.0855251684755-0.487628706121-0.01570558322760.665090289962-0.03410329988430.000641933200411-0.139238411773-0.1985560646290.04391252684041.25613445945-0.2213545168140.3074095593311.332677619710.2462649428320.569311082947-13.492333587210.534385337457.2119437522
171.57413030473-0.3641808338211.294226094992.502451233760.4142609938282.240346828590.155177999732-0.3230187341780.1668042317890.170035676471-0.02708914049390.198219528551-0.323632387471-0.176436608217-0.255693934410.818442624119-0.2032355636960.2472327587231.025514284250.09998305263740.65205779827-15.1758981042-0.79367061557554.2641798999
185.59102664067-2.40447948446-3.877833709613.570730593425.403524930478.191513295-0.233602610276-1.23790019426-0.2544960416770.8813886401990.271135685596-1.05017908381.983741956890.274305079905-0.0294735840610.9662141604690.05242319586330.03885146532061.11287447850.4030717735320.87313552036716.87717354255.3259410812843.7958173374
191.38125849679-0.9020173962592.360688623452.16810273050.2887879487626.23176696145-0.0758011643937-0.3949685027070.3380173396020.173747253607-0.0896746429877-0.513827015057-0.1548194859590.5873205508240.2020371013710.715499855261-0.2617649276510.01970682072811.138271502190.07812604065640.70885260277219.232272836611.579912018946.1773902239
202.78543377654-1.817211617172.06605843512.35779482840.6731446157155.070368110260.243567719084-0.3294049303630.280869060234-0.0936564713765-0.497848100359-0.3945303365660.005604494942391.108093305030.308595498550.547362999419-0.1922540324440.126538705990.8298572378330.08943885361520.81144037062116.910115604913.558948941532.1298559383
213.04567773271-1.603343435611.604327203722.774196961720.3663194258856.83999405615-0.250424644619-0.6225172007120.5257123941930.136402284552-0.343668832691-0.527077130756-0.898153984740.5532799601990.4254520934370.860458154769-0.2940147280450.1127392034360.864966489878-0.177229117770.89143843432613.53985981619.239009143238.6964403886
222.281056038612.16728135961-1.567257051342.06266509649-1.531988639611.696334200110.967290354736-1.266237444620.1301041350911.12098289979-0.784139753846-0.789193186151-0.1691646460521.27071799981-0.1529030230040.770430587721-0.330753505252-0.06340546410131.486205844790.1266163757060.98448612482222.660013559415.964712540341.75053296
233.442866421592.3306615439-1.520706891484.41486004778-1.163982764615.88520398571.25174860022-1.180970826490.4864060661471.30745265569-0.729942190801-0.0342166994687-0.2829198571730.512804949054-0.3350233384650.690121695334-0.3334175232620.01457112672771.26354831076-0.07635673164780.74821394563510.434979014613.718079846744.3219241775
243.723449167353.27347378002-3.380250554563.48705280213-1.679210813515.786727630880.145077357747-0.4225237063230.1270832300480.113494660629-0.186290934394-0.382422673780.1552539358390.417051430845-0.1211311512840.318161734941-0.03399158776510.01036439930390.8269826284650.1841825894050.53323695148814.58108249910.739438265927.3026990355
250.325995553772-0.4292830505690.3909412008081.25762195655-0.9241020865560.72103046645-0.448456350165-0.5982177550990.255007681520.2190707530651.068737064930.3905803568710.382318137937-0.328407941703-0.5923860845571.05444136895-0.284773611215-0.0005264783154241.97061951199-0.04321877180540.7192472638557.062699492019.8133236825562.1556535254
268.512051697941.1717594777-2.882305563669.82494822347-5.780488004693.97344724444-0.0531276659255-1.28199342908-0.1695506896810.624015307344-0.2593906377820.04550006271930.447114458240.6807286836560.4116716595841.09195666738-0.08406942071830.0105494848071.344569567230.1413452740910.620909333368-3.0586390017-4.6428178323965.6751596235
276.306137175021.95402307813-1.162785282546.95565958954-2.107056686979.103447605110.702268056548-1.028726034210.2072613547920.6559041543550.4171141379820.4891796196560.826350435399-0.624454029396-1.008422128180.98273275985-0.141631556349-0.1032499332931.196023481370.02911884000510.916280013117-3.04351831185-0.35807094294364.9501977093
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 176 )AA7 - 1761 - 170
22chain 'A' and (resid 177 through 283 )AA177 - 283171 - 277
33chain 'B' and (resid 1 through 6 )BE1 - 61 - 6
44chain 'B' and (resid 7 through 20 )BE7 - 207 - 20
55chain 'B' and (resid 21 through 31 )BE21 - 3121 - 31
66chain 'B' and (resid 32 through 37 )BE32 - 3732 - 37
77chain 'B' and (resid 38 through 47 )BE38 - 4738 - 47
88chain 'B' and (resid 48 through 57 )BE48 - 5748 - 57
99chain 'B' and (resid 58 through 72 )BE58 - 7258 - 72
1010chain 'B' and (resid 73 through 83 )BE73 - 8373 - 83
1111chain 'B' and (resid 84 through 91 )BE84 - 9184 - 91
1212chain 'B' and (resid 92 through 99 )BE92 - 9992 - 99
1313chain 'C' and (resid 11 through 92 )CF11 - 921 - 82
1414chain 'C' and (resid 93 through 132 )CF93 - 13283 - 122
1515chain 'C' and (resid 133 through 158 )CF133 - 158123 - 148
1616chain 'C' and (resid 159 through 176 )CF159 - 176149 - 166
1717chain 'C' and (resid 177 through 248 )CF177 - 248167 - 238
1818chain 'D' and (resid 2 through 15 )DG2 - 151 - 14
1919chain 'D' and (resid 16 through 27 )DG16 - 2715 - 26
2020chain 'D' and (resid 28 through 41 )DG28 - 4127 - 40
2121chain 'D' and (resid 42 through 63 )DG42 - 6341 - 62
2222chain 'D' and (resid 64 through 79 )DG64 - 7963 - 78
2323chain 'D' and (resid 80 through 96 )DG80 - 9679 - 95
2424chain 'D' and (resid 97 through 108 )DG97 - 10896 - 107
2525chain 'D' and (resid 109 through 122 )DG109 - 122108 - 121
2626chain 'D' and (resid 123 through 161 )DG123 - 161122 - 160
2727chain 'D' and (resid 162 through 193 )DG162 - 193161 - 192

+
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