[English] 日本語
Yorodumi
- PDB-5jzi: Crystal structure of 1406 TCR bound to HLA-A2 with HCV 1406-1415 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jzi
TitleCrystal structure of 1406 TCR bound to HLA-A2 with HCV 1406-1415 antigen peptide
Components
  • Beta-2-microglobulin
  • HCV1406 TCR alpha chain
  • HCV1406 TCR beta chain
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • KLV peptide
KeywordsProtein binding/Immune System / HCV1406 TCR / HLA-A2 / HCV NS3:1406-1415 peptide / decapeptide / Protein binding / Immune System complex / Protein binding-Immune System complex
Function / homology
Function and homology information


positive regulation of hexokinase activity / symbiont-mediated perturbation of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / hepacivirin / TBC/RABGAPs / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target ...positive regulation of hexokinase activity / symbiont-mediated perturbation of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / hepacivirin / TBC/RABGAPs / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / CD8 receptor binding / symbiont-mediated suppression of host TRAF-mediated signal transduction / positive regulation of cytokinesis / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / negative regulation of protein secretion / detection of bacterium / T cell receptor binding / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / 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 / SH3 domain binding / kinase binding / specific granule lumen / positive regulation of type II interferon production / 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 / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / nucleoside-triphosphate phosphatase / negative regulation of neuron projection development / channel activity / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / monoatomic ion transmembrane transport / protein homotetramerization
Similarity search - Function
Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : ...Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / 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 / DEAD box, Flavivirus / Flavivirus DEAD domain / 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. / helicase superfamily c-terminal domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Genome polyprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, Y. / Piepenbrink, K.H. / Baker, B.M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: How an alloreactive T-cell receptor achieves peptide and MHC specificity.
Authors: Wang, Y. / Singh, N.K. / Spear, T.T. / Hellman, L.M. / Piepenbrink, K.H. / McMahan, R.H. / Rosen, H.R. / Vander Kooi, C.W. / Nishimura, M.I. / Baker, B.M.
History
DepositionMay 16, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionMay 31, 2017ID: 4ZEZ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 31, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Jun 24, 2020Group: Advisory / Category: pdbx_database_PDB_obs_spr / Item: _pdbx_database_PDB_obs_spr.replace_pdb_id
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: KLV peptide
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: KLV peptide
D: HCV1406 TCR alpha chain
E: HCV1406 TCR beta chain
I: HCV1406 TCR alpha chain
J: HCV1406 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)193,36510
Polymers193,36510
Non-polymers00
Water1,74797
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: KLV peptide
D: HCV1406 TCR alpha chain
E: HCV1406 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)96,6835
Polymers96,6835
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: KLV peptide
I: HCV1406 TCR alpha chain
J: HCV1406 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)96,6835
Polymers96,6835
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.760, 128.760, 223.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 4 types, 8 molecules AFBGDIEJ

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: P61769
#4: Protein HCV1406 TCR alpha chain


Mass: 23914.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#5: Protein HCV1406 TCR beta chain


Mass: 28036.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

-
Protein/peptide / Non-polymers , 2 types, 99 molecules CH

#3: Protein/peptide KLV peptide


Mass: 998.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: P27958*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 13% PEG 3350, 0.1M Sodium Cacodylate, 0.2m Ammonium Sulfate, 3% w/v 1,5-Diaminopentane dihydrochloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→48.72 Å / Num. obs: 78081 / % possible obs: 86 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 1.13

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
PHENIXdev_1958phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MRM

3mrm


Resolution: 2.5→37.17 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.232 1384 1.86 %
Rwork0.1955 --
obs0.2012 74522 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13228 0 0 97 13325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513589
X-RAY DIFFRACTIONf_angle_d0.76818383
X-RAY DIFFRACTIONf_dihedral_angle_d11.264956
X-RAY DIFFRACTIONf_chiral_restr0.0281926
X-RAY DIFFRACTIONf_plane_restr0.0042390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.59030.28351360.29197198X-RAY DIFFRACTION97
2.5903-2.69390.31741360.29347156X-RAY DIFFRACTION97
2.6939-2.81630.29851380.28757254X-RAY DIFFRACTION98
2.8163-2.96460.29241400.26927199X-RAY DIFFRACTION98
2.9646-3.150.25321360.25137242X-RAY DIFFRACTION98
3.15-3.39270.26251370.23377304X-RAY DIFFRACTION98
3.3927-3.73320.22441390.21227268X-RAY DIFFRACTION98
3.7332-4.27130.2341390.17927335X-RAY DIFFRACTION98
4.2713-5.37320.21161390.14257415X-RAY DIFFRACTION98
5.3732-25.63850.19881440.16537646X-RAY DIFFRACTION98
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)
13.161-0.59120.43992.6652-0.29233.2765-0.1274-0.34340.17570.18640.0422-0.0096-0.3915-0.04540.0570.3030.05930.00820.3017-0.10170.2842-88.107977.90425.72
22.8948-1.79180.08361.597-0.01042.27530.02940.0447-0.16460.6510.42261.4025-0.3187-0.1543-0.37141.07710.07160.31510.8704-0.12991.5874-96.6406106.161243.4898
33.01560.4750.62522.2321-0.04683.5675-0.3103-0.11730.9658-0.3264-0.1506-0.0262-0.64930.33250.5060.76730.0842-0.04380.5006-0.04590.8904-81.5301103.525728.6518
40.6619-0.26240.14892.3383-2.18313.5331-0.01250.03460.181-0.25720.0768-0.34110.72850.06690.11860.26240.10130.07740.58360.0010.3848-87.868970.212422.6497
52.4990.20690.51221.66140.16252.4615-0.20480.62310.302-0.10720.108-0.0681-0.29490.46950.07230.3294-0.1577-0.00860.65340.19170.4666-41.197175.675710.6636
60.8351-0.39760.60030.66090.44521.5468-0.05760.39970.77010.23540.8846-0.21130.0998-0.1085-0.85760.9719-0.05780.04920.83950.25521.4212-31.9756100.1845-12.8804
72.2927-0.4271.62130.8490.83832.8373-0.40730.16340.9337-0.1657-0.1818-0.0916-0.7251-0.23220.56960.7808-0.0531-0.01650.63170.19811.171-46.7697100.95144.5188
82.3353-1.5583-0.18562.95230.07891.1122-0.13820.7605-0.8776-0.1429-0.3497-0.35010.25930.22980.5290.49-0.1380.1910.60590.07730.6054-41.749868.909514.683
92.0335-0.37150.82684.70110.39743.968-0.0144-0.2828-0.34240.3892-0.06690.17460.7418-0.08290.09540.3803-0.04060.05320.3160.04730.2971-81.476547.077122.9143
101.21060.86430.59581.8554-0.20372.27140.12730.1939-0.1360.43630.0841-0.490.81570.1675-0.24931.15150.2548-0.07680.5002-0.06620.5168-66.71619.5157.0306
114.9846-1.7334-1.29352.20010.68813.94710.10780.3978-0.1583-0.1396-0.13180.25890.0386-0.22410.02450.2803-0.0016-0.04940.2666-0.00860.2047-75.931158.98335.4376
122.34360.87630.02655.5157-1.051.2639-0.00720.0079-0.07470.04120.1506-0.07050.25510.067-0.12030.65420.06950.0130.4474-0.05120.2276-70.637130.9943-5.917
131.0342-0.2866-0.01824.0266-0.44732.62540.0210.2534-0.1415-0.2791-0.1039-0.02830.30540.19560.10370.29380.01920.01480.4042-0.05310.3485-48.61546.274417.635
145.1532-0.43971.07273.69010.25234.35730.23310.0798-0.1574-0.0194-0.10490.41180.41170.0713-0.12350.5971-0.03610.04880.3170.00620.3305-62.965421.409336.5252
154.33881.139-1.94532.83310.30243.5827-0.03950.012-0.27140.11710.0726-0.33820.15830.258-0.02790.2706-0.0237-0.07460.32250.01540.2475-54.158660.746333.345
162.8222-1.6265-0.12356.3226-0.67791.37690.0867-0.0793-0.062-0.1735-0.04330.19370.11520.0733-0.05580.4219-0.06320.06170.3907-0.01650.1652-59.782134.706148.2353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 272 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 99 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 10 )
5X-RAY DIFFRACTION5chain 'F' and (resid 1 through 180)
6X-RAY DIFFRACTION6chain 'F' and (resid 181 through 274 )
7X-RAY DIFFRACTION7chain 'G' and (resid 0 through 99 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 10 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 117 )
10X-RAY DIFFRACTION10chain 'D' and (resid 118 through 208 )
11X-RAY DIFFRACTION11chain 'E' and (resid 1 through 111 )
12X-RAY DIFFRACTION12chain 'E' and (resid 112 through 240 )
13X-RAY DIFFRACTION13chain 'I' and (resid 1 through 117)
14X-RAY DIFFRACTION14chain 'I' and (resid 118 through 208 )
15X-RAY DIFFRACTION15chain 'J' and (resid 1 through 111 )
16X-RAY DIFFRACTION16chain 'J' and (resid 112 through 240 )

+
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