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- PDB-9k2r: Human T cell receptor (TRAV24*01/TRBV27*01) in complex with HLA-C... -

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Basic information

Entry
Database: PDB / ID: 9k2r
TitleHuman T cell receptor (TRAV24*01/TRBV27*01) in complex with HLA-C*1202 and IY11 peptide
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • T cell receptor alpha chain
  • T cell receptor beta chain
  • peptide from p51 RT
KeywordsIMMUNE SYSTEM / CD8+ T cells / HIV-1 / escape mutant / KIR2DL2 / TCR / HLA
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / HIV-1 retropepsin ...antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / HIV-1 retropepsin / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / symbiont-mediated activation of host apoptosis / peptide antigen assembly with MHC class II protein complex / retroviral ribonuclease H / exoribonuclease H / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / exoribonuclease H activity / 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 erythrocyte differentiation / regulation of iron ion transport / 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 / host multivesicular body / 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 / DNA integration / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / viral genome integration into host DNA / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / Modulation by Mtb of host immune system / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / RNA-directed DNA polymerase activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / RNA-DNA hybrid ribonuclease activity / MHC class II protein complex binding / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / host cell / negative regulation of neuron projection development / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination / protein homotetramerization / amyloid fibril formation / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / DNA-directed DNA polymerase activity / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / symbiont-mediated suppression of host gene expression / viral translational frameshifting / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / lipid binding / Neutrophil degranulation / symbiont entry into host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / proteolysis / extracellular space
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / Reverse transcriptase thumb / Reverse transcriptase thumb domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / Reverse transcriptase thumb / Reverse transcriptase thumb domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
MHC class I antigen / Gag-Pol polyprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsChikata, T. / Kuroki, K. / Kuse, N. / Kliszczak, A. / Paes, W. / Tomioka, N. / Parker, R. / Aflalo, A. / Akahoshi, T. / Yamashita, R. ...Chikata, T. / Kuroki, K. / Kuse, N. / Kliszczak, A. / Paes, W. / Tomioka, N. / Parker, R. / Aflalo, A. / Akahoshi, T. / Yamashita, R. / Sakata, R. / Kusaka, H. / Watanabe, Y. / Nicastri, A. / Matsubara, H. / Ose, T. / Kita, S. / Oka, S. / Gatanaga, H. / Lin, Z. / Ternette, N. / Borrow, P. / Maenaka, K. / Takiguchi, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)17fk0410302h0003 Japan
Japan Agency for Medical Research and Development (AMED)21fk0410032h0003 Japan
Japan Society for the Promotion of Science (JSPS)20H03726 Japan
CitationJournal: To Be Published
Title: Human T cell receptor (TRAV24*01/TRBV27*01) in complex with HLA-C*1202 and IY11 peptide
Authors: Chikata, T. / Kuroki, K. / Kuse, N. / Kliszczak, A. / Paes, W. / Tomioka, N. / Parker, R. / Aflalo, A. / Akahoshi, T. / Yamashita, R. / Sakata, R. / Kusaka, H. / Watanabe, Y. / Nicastri, A. ...Authors: Chikata, T. / Kuroki, K. / Kuse, N. / Kliszczak, A. / Paes, W. / Tomioka, N. / Parker, R. / Aflalo, A. / Akahoshi, T. / Yamashita, R. / Sakata, R. / Kusaka, H. / Watanabe, Y. / Nicastri, A. / Matsubara, H. / Ose, T. / Kita, S. / Oka, S. / Gatanaga, H. / Lin, Z. / Ternette, N. / Borrow, P. / Maenaka, K. / Takiguchi, M.
History
DepositionOct 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: peptide from p51 RT
D: MHC class I antigen
E: Beta-2-microglobulin
F: peptide from p51 RT
G: MHC class I antigen
H: Beta-2-microglobulin
I: peptide from p51 RT
J: T cell receptor alpha chain
K: T cell receptor beta chain
L: T cell receptor alpha chain
M: T cell receptor beta chain
N: T cell receptor alpha chain
O: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)286,43115
Polymers286,43115
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: peptide from p51 RT
J: T cell receptor alpha chain
K: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,4775
Polymers95,4775
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: peptide from p51 RT
L: T cell receptor alpha chain
M: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,4775
Polymers95,4775
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: MHC class I antigen
H: Beta-2-microglobulin
I: peptide from p51 RT
N: T cell receptor alpha chain
O: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,4775
Polymers95,4775
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)207.827, 344.872, 134.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 104 or resid 110 through 277))
d_2ens_1(chain "D" and (resid 3 through 17 or resid 20 through 277))
d_3ens_1(chain "G" and (resid 3 through 104 or resid 110 through 277))
d_1ens_2(chain "B" and resid 1 through 99)
d_2ens_2chain "E"
d_3ens_2chain "H"
d_1ens_3chain "C"
d_2ens_3chain "F"
d_3ens_3chain "I"
d_1ens_4(chain "J" and (resid 1 through 141 or resid 144 through 146 or resid 150 through 201))
d_2ens_4(chain "L" and (resid 1 through 190 or resid 193 through 201))
d_1ens_5(chain "K" and (resid 2 through 178 or resid 181 through 221 or resid 224 through 241))
d_2ens_5(chain "M" and (resid 2 through 178 or resid 181 through 221 or resid 224 through 241))
d_3ens_5(chain "O" and resid 2 through 241)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERLEULEUAA3 - 1041 - 102
d_12ens_1LEULEUPROPROAA110 - 277108 - 275
d_21ens_1SERSERGLYGLYDD3 - 171 - 15
d_22ens_1GLUGLUPROPRODD20 - 27718 - 275
d_31ens_1SERSERLEULEUGG3 - 1041 - 102
d_32ens_1LEULEUPROPROGG110 - 277108 - 275
d_11ens_2METMETASPASPBB1 - 991 - 99
d_21ens_2METMETASPASPEE1 - 991 - 99
d_31ens_2METMETASPASPHH1 - 991 - 99
d_11ens_3ILEILETYRTYRCC1 - 111 - 11
d_21ens_3ILEILETYRTYRFF1 - 111 - 11
d_31ens_3ILEILETYRTYRII1 - 111 - 11
d_11ens_4ILEILEASPASPJJ1 - 1411 - 141
d_12ens_4THRTHRVALVALJJ144 - 146144 - 146
d_13ens_4LYSLYSPROPROJJ150 - 201150 - 201
d_21ens_4ILEILEASNASNLL1 - 1901 - 190
d_22ens_4ILEILEPROPROLL193 - 201193 - 201
d_11ens_5VALVALPROPROKK2 - 1782 - 178
d_12ens_5ASNASNTHRTHRKK181 - 221181 - 221
d_13ens_5ARGARGASPASPKK224 - 241224 - 241
d_21ens_5VALVALPROPROMM2 - 1782 - 178
d_22ens_5ASNASNTHRTHRMM181 - 221181 - 221
d_23ens_5ARGARGASPASPMM224 - 241224 - 241
d_31ens_5VALVALASPASPOO2 - 2412 - 241

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(-0.495508419267, -0.868371651128, 0.0200519812781), (-0.866239887023, 0.495730336182, 0.0622887784372), (-0.0640301847983, 0.0134947881446, -0.997856716231)155.722234527, 78.8376030609, 1.31090034899
2given(0.508650523457, -0.857324924036, -0.0791746147062), (-0.857949474445, -0.512416632408, 0.0367681129634), (-0.0720926090933, 0.0492256991712, -0.996182456308)54.2857698309, 90.0061854037, 66.3359447364
3given(-0.509930755289, -0.859821350552, -0.0260359356498), (-0.859208765831, 0.507636796446, 0.0637587610728), (-0.0416043450895, 0.054882857327, -0.997625656467)157.103907905, 77.9754998512, -0.889980520385
4given(0.50552269649, -0.85668019593, -0.102692965849), (-0.861822131284, -0.507056065217, -0.0125204135731), (-0.0413451008359, 0.0948324239263, -0.994634301645)54.8524698631, 90.9740465923, 63.4276754291
5given(-0.523194032578, -0.851754191744, 0.0279785832657), (-0.850295510478, 0.523936517051, 0.0498805669686), (-0.0571449834703, 0.00230715123922, -0.998363224442)156.089606784, 76.9448638149, 1.56324673105
6given(0.494916921361, -0.865937584595, -0.0721757614169), (-0.86618770252, -0.49825047381, 0.0382796205816), (-0.0691093695092, 0.0435725249902, -0.996657077491)55.1081377529, 89.6281729436, 66.4945035952
7given(-0.503199118936, -0.862358126156, 0.0559384389686), (-0.860715352576, 0.505918730668, 0.0567037899895), (-0.0771992781199, -0.0196137760564, -0.996822738127)155.083613991, 78.6332412488, 3.78943759376
8given(-0.506008168221, -0.861592582706, 0.0401740602829), (-0.861644473439, 0.507049300766, 0.0216750544455), (-0.0390452953154, -0.0236480024223, -0.998957575123)155.404773861, 79.2349573769, 2.16471332472
9given(0.491593566142, -0.869277274329, -0.0518920616566), (-0.868937333605, -0.493577603327, 0.0364562719076), (-0.0573033681002, 0.0271692809758, -0.997987051106)55.3321823786, 89.4884491545, 66.8180831378

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Components

#1: Protein MHC class I antigen


Mass: 31900.992 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C / Production host: Escherichia coli (E. coli) / References: UniProt: A0A165EYK7
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide peptide from p51 RT


Mass: 1319.547 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
References: UniProt: P12499
#4: Protein T cell receptor alpha chain


Mass: 23001.473 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein T cell receptor beta chain


Mass: 27375.621 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH7.0, 1.6M ammonium sulfate, 0.2M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.98→44.5 Å / Num. obs: 98231 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 66.06 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.1
Reflection shellResolution: 2.98→3.03 Å / Num. unique obs: 4820 / CC1/2: 0.595

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→44.5 Å / SU ML: 0.3663 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.7399
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 4555 4.64 %
Rwork0.2074 93591 -
obs0.2085 98146 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.5 Å2
Refinement stepCycle: LAST / Resolution: 2.98→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19681 0 0 0 19681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002820207
X-RAY DIFFRACTIONf_angle_d0.571627448
X-RAY DIFFRACTIONf_chiral_restr0.04282859
X-RAY DIFFRACTIONf_plane_restr0.0053598
X-RAY DIFFRACTIONf_dihedral_angle_d12.54127418
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.711388199068
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.704750013187
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.702707769276
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.628533035014
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.152787584965
ens_3d_3CCX-RAY DIFFRACTIONTorsion NCS0.17124561548
ens_4d_2JJX-RAY DIFFRACTIONTorsion NCS0.979976739581
ens_5d_2KKX-RAY DIFFRACTIONTorsion NCS0.544663957757
ens_5d_3KKX-RAY DIFFRACTIONTorsion NCS0.593302119133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.010.35271300.34473116X-RAY DIFFRACTION99.78
3.01-3.050.34841600.33193098X-RAY DIFFRACTION99.91
3.05-3.090.33781540.31443045X-RAY DIFFRACTION99.91
3.09-3.130.3251540.31153120X-RAY DIFFRACTION99.97
3.13-3.170.32141340.29643107X-RAY DIFFRACTION99.85
3.17-3.210.32751550.28743067X-RAY DIFFRACTION99.88
3.21-3.260.32561570.27563135X-RAY DIFFRACTION99.85
3.26-3.30.30571370.28013089X-RAY DIFFRACTION99.75
3.3-3.360.28731470.27563136X-RAY DIFFRACTION99.97
3.36-3.410.29941470.27513053X-RAY DIFFRACTION99.53
3.41-3.470.28681760.2613073X-RAY DIFFRACTION99.63
3.47-3.530.26051750.23373042X-RAY DIFFRACTION98.26
3.53-3.60.24471460.22523082X-RAY DIFFRACTION99.85
3.6-3.670.27161430.21573099X-RAY DIFFRACTION99.97
3.67-3.750.23051560.20583111X-RAY DIFFRACTION99.91
3.75-3.840.21882050.20363077X-RAY DIFFRACTION99.85
3.84-3.940.21861560.19823079X-RAY DIFFRACTION99.81
3.94-4.040.23671370.19543152X-RAY DIFFRACTION99.97
4.04-4.160.22191300.19053129X-RAY DIFFRACTION99.97
4.16-4.30.20531220.17093146X-RAY DIFFRACTION99.94
4.3-4.450.18391530.15953125X-RAY DIFFRACTION99.97
4.45-4.630.18051750.14743104X-RAY DIFFRACTION100
4.63-4.840.18541390.14813169X-RAY DIFFRACTION100
4.84-5.090.17171560.15853106X-RAY DIFFRACTION100
5.09-5.410.21621480.17283158X-RAY DIFFRACTION100
5.41-5.830.22031250.1883178X-RAY DIFFRACTION100
5.83-6.410.2261550.21753176X-RAY DIFFRACTION100
6.41-7.340.26551560.2123118X-RAY DIFFRACTION98.11
7.34-9.230.18481760.18383194X-RAY DIFFRACTION100
9.23-44.50.20081510.19933307X-RAY DIFFRACTION98.8

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