[English] 日本語
Yorodumi
- PDB-7rm4: Neoantigen p53R175H-specific TCR 6-11 binds to p53R175H-HLA-A2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rm4
TitleNeoantigen p53R175H-specific TCR 6-11 binds to p53R175H-HLA-A2
Components
  • 6-11 T cell receptor alpha chain
  • 6-11 T cell receptor beta chain
  • Beta-2-microglobulin
  • Cellular tumor antigen p53 peptide
  • HLA class I histocompatibility antigen, A alpha chain
KeywordsIMMUNE SYSTEM / TCR-pMHC / Neoantigen / Cancer
Function / homology
Function and homology information


negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria ...negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / regulation of cell cycle G2/M phase transition / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of thymocyte apoptotic process / positive regulation of mitochondrial membrane permeability / germ cell nucleus / regulation of fibroblast apoptotic process / bone marrow development / cellular response to actinomycin D / circadian behavior / histone deacetylase regulator activity / positive regulation of programmed necrotic cell death / : / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / T cell proliferation involved in immune response / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of CD8-positive, alpha-beta T cell proliferation / Regulation of TP53 Activity through Association with Co-factors / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / thymocyte apoptotic process / ER overload response / TP53 Regulates Transcription of Caspase Activators and Caspases / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cardiac septum morphogenesis / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / B cell lineage commitment / Golgi medial cisterna / entrainment of circadian clock by photoperiod / negative regulation of DNA replication / Zygotic genome activation (ZGA) / negative regulation of mitophagy / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / necroptotic process / PI5P Regulates TP53 Acetylation / CD8 receptor binding / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of release of cytochrome c from mitochondria / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / protection from natural killer cell mediated cytotoxicity / rRNA transcription / negative regulation of reactive oxygen species metabolic process / TFIID-class transcription factor complex binding / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional Regulation by VENTX / cellular response to UV-C / beta-2-microglobulin binding / neuroblast proliferation / viral process / endoplasmic reticulum exit site / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / TAP binding / replicative senescence / positive regulation of RNA polymerase II transcription preinitiation complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Pyroptosis / general transcription initiation factor binding / chromosome organization / positive regulation of execution phase of apoptosis / hematopoietic stem cell differentiation / detection of bacterium / embryonic organ development / type II interferon-mediated signaling pathway / 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 / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / response to X-ray / hematopoietic progenitor cell differentiation / somitogenesis / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding
Similarity search - Function
Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain ...Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / 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 / 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
HLA class I histocompatibility antigen, A alpha chain / Cellular tumor antigen p53 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsWu, D. / Mariuzza, R.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI129893 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126299 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: T cell receptors employ diverse strategies to target a p53 cancer neoantigen.
Authors: Wu, D. / Gowathaman, R. / Pierce, B.G. / Mariuzza, R.A.
History
DepositionJul 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 16, 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 alpha chain
B: Beta-2-microglobulin
C: Cellular tumor antigen p53 peptide
D: 6-11 T cell receptor beta chain
E: 6-11 T cell receptor alpha chain
F: HLA class I histocompatibility antigen, A alpha chain
G: Beta-2-microglobulin
H: Cellular tumor antigen p53 peptide
I: 6-11 T cell receptor beta chain
J: 6-11 T cell receptor alpha chain
K: HLA class I histocompatibility antigen, A alpha chain
L: Beta-2-microglobulin
M: Cellular tumor antigen p53 peptide
N: 6-11 T cell receptor beta chain
O: 6-11 T cell receptor alpha chain
P: HLA class I histocompatibility antigen, A alpha chain
Q: Beta-2-microglobulin
R: Cellular tumor antigen p53 peptide
S: 6-11 T cell receptor beta chain
T: 6-11 T cell receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)383,41120
Polymers383,41120
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Cellular tumor antigen p53 peptide
D: 6-11 T cell receptor beta chain
E: 6-11 T cell receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)95,8535
Polymers95,8535
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A alpha chain
G: Beta-2-microglobulin
H: Cellular tumor antigen p53 peptide
I: 6-11 T cell receptor beta chain
J: 6-11 T cell receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)95,8535
Polymers95,8535
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: HLA class I histocompatibility antigen, A alpha chain
L: Beta-2-microglobulin
M: Cellular tumor antigen p53 peptide
N: 6-11 T cell receptor beta chain
O: 6-11 T cell receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)95,8535
Polymers95,8535
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: HLA class I histocompatibility antigen, A alpha chain
Q: Beta-2-microglobulin
R: Cellular tumor antigen p53 peptide
S: 6-11 T cell receptor beta chain
T: 6-11 T cell receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)95,8535
Polymers95,8535
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.226, 55.144, 304.877
Angle α, β, γ (deg.)90.000, 98.740, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resid 1 through 57 or (resid 58...
21chain F
31chain K
41chain P
12chain B
22(chain G and resid 1 through 99)
32chain L
42chain Q
13chain C
23chain H
33chain M
43chain R
14(chain D and (resid 2 through 227 or (resid 228...
24(chain I and (resid 2 through 82 or (resid 83...
34(chain N and (resid 2 through 82 or (resid 83...
44(chain S and (resid 2 through 82 or (resid 83...
15chain E
25chain J
35chain O
45chain T

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYPROPRO(chain A and (resid 1 through 57 or (resid 58...AA1 - 571 - 57
121GLUGLUGLUGLU(chain A and (resid 1 through 57 or (resid 58...AA5858
131GLYGLYGLUGLU(chain A and (resid 1 through 57 or (resid 58...AA1 - 2751 - 275
141GLYGLYGLUGLU(chain A and (resid 1 through 57 or (resid 58...AA1 - 2751 - 275
151GLYGLYGLUGLU(chain A and (resid 1 through 57 or (resid 58...AA1 - 2751 - 275
161GLYGLYGLUGLU(chain A and (resid 1 through 57 or (resid 58...AA1 - 2751 - 275
211GLYGLYGLUGLUchain FFF1 - 2751 - 275
311GLYGLYGLUGLUchain KKK1 - 2751 - 275
411GLYGLYGLUGLUchain PPP1 - 2751 - 275
112METMETMETMETchain BBB1 - 1001 - 100
212METMETASPASP(chain G and resid 1 through 99)GG1 - 991 - 99
312METMETMETMETchain LLL1 - 1001 - 100
412METMETMETMETchain QQQ1 - 1001 - 100
113HISHISCYSCYSchain CCC1 - 91 - 9
213HISHISCYSCYSchain HHH1 - 91 - 9
313HISHISCYSCYSchain MMM1 - 91 - 9
413HISHISCYSCYSchain RRR1 - 91 - 9
114ALAALAASPASP(chain D and (resid 2 through 227 or (resid 228...DD2 - 2273 - 228
124ARGARGALAALA(chain D and (resid 2 through 227 or (resid 228...DD228 - 229229 - 230
134ALAALAALAALA(chain D and (resid 2 through 227 or (resid 228...DD2 - 2443 - 245
144ALAALAALAALA(chain D and (resid 2 through 227 or (resid 228...DD2 - 2443 - 245
154ALAALAALAALA(chain D and (resid 2 through 227 or (resid 228...DD2 - 2443 - 245
164ALAALAALAALA(chain D and (resid 2 through 227 or (resid 228...DD2 - 2443 - 245
214ALAALAALAALA(chain I and (resid 2 through 82 or (resid 83...II2 - 823 - 83
224LYSLYSLYSLYS(chain I and (resid 2 through 82 or (resid 83...II8384
234ALAALAALAALA(chain I and (resid 2 through 82 or (resid 83...II2 - 2443 - 245
244ALAALAALAALA(chain I and (resid 2 through 82 or (resid 83...II2 - 2443 - 245
254ALAALAALAALA(chain I and (resid 2 through 82 or (resid 83...II2 - 2443 - 245
264ALAALAALAALA(chain I and (resid 2 through 82 or (resid 83...II2 - 2443 - 245
314ALAALAALAALA(chain N and (resid 2 through 82 or (resid 83...NN2 - 823 - 83
324LYSLYSLYSLYS(chain N and (resid 2 through 82 or (resid 83...NN8384
334ALAALAALAALA(chain N and (resid 2 through 82 or (resid 83...NN2 - 2443 - 245
344ALAALAALAALA(chain N and (resid 2 through 82 or (resid 83...NN2 - 2443 - 245
354ALAALAALAALA(chain N and (resid 2 through 82 or (resid 83...NN2 - 2443 - 245
414ALAALAALAALA(chain S and (resid 2 through 82 or (resid 83...SS2 - 823 - 83
424LYSLYSLYSLYS(chain S and (resid 2 through 82 or (resid 83...SS8384
434ALAALAALAALA(chain S and (resid 2 through 82 or (resid 83...SS2 - 2443 - 245
115LYSLYSPROPROchain EEE3 - 2024 - 203
215LYSLYSPROPROchain JJJ3 - 2024 - 203
315LYSLYSPROPROchain OOO3 - 2024 - 203
415LYSLYSPROPROchain TTT3 - 2024 - 203

NCS ensembles :
ID
1
2
3
4
5

-
Components

#1: Protein
HLA class I histocompatibility antigen, A alpha chain / Human leukocyte antigen A / HLA-A


Mass: 31854.203 Da / Num. of mol.: 4 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04439
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide
Cellular tumor antigen p53 peptide / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 1114.320 Da / Num. of mol.: 4 / Mutation: R175H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04637
#4: Protein
6-11 T cell receptor beta chain


Mass: 27662.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 6-11 T cell receptor beta chain / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#5: Protein
6-11 T cell receptor alpha chain


Mass: 23342.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 6-11 T cell receptor alpha chain / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% (w/v) PEG 3350, 0.1 M Bis-Tris propane (pH 8.5), and 0.2 M Potassium thiocyanate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.33→49.319 Å / Num. obs: 60837 / % possible obs: 92.6 % / Redundancy: 4.8 % / CC1/2: 0.992 / Net I/σ(I): 10.3
Reflection shellResolution: 3.33→3.45 Å / Num. unique obs: 4526 / CC1/2: 0.737

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WKF, 6OVN, 6VR5

5wkf

6ovn

6vr5


Resolution: 3.33→49.319 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2949 2703 4.65 %
Rwork0.237 55378 -
obs0.2397 58081 92.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.11 Å2 / Biso mean: 50.5848 Å2 / Biso min: 10.05 Å2
Refinement stepCycle: final / Resolution: 3.33→49.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26474 0 0 0 26474
Num. residues----3308
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3376X-RAY DIFFRACTION2.015TORSIONAL
12F3376X-RAY DIFFRACTION2.015TORSIONAL
13K3376X-RAY DIFFRACTION2.015TORSIONAL
14P3376X-RAY DIFFRACTION2.015TORSIONAL
21B1196X-RAY DIFFRACTION2.015TORSIONAL
22G1196X-RAY DIFFRACTION2.015TORSIONAL
23L1196X-RAY DIFFRACTION2.015TORSIONAL
24Q1196X-RAY DIFFRACTION2.015TORSIONAL
31C104X-RAY DIFFRACTION2.015TORSIONAL
32H104X-RAY DIFFRACTION2.015TORSIONAL
33M104X-RAY DIFFRACTION2.015TORSIONAL
34R104X-RAY DIFFRACTION2.015TORSIONAL
41D2912X-RAY DIFFRACTION2.015TORSIONAL
42I2912X-RAY DIFFRACTION2.015TORSIONAL
43N2912X-RAY DIFFRACTION2.015TORSIONAL
44S2912X-RAY DIFFRACTION2.015TORSIONAL
51E2400X-RAY DIFFRACTION2.015TORSIONAL
52J2400X-RAY DIFFRACTION2.015TORSIONAL
53O2400X-RAY DIFFRACTION2.015TORSIONAL
54T2400X-RAY DIFFRACTION2.015TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.33-3.39050.39121150.3319209167
3.3905-3.45570.39031290.3194241377
3.4557-3.52630.38291310.3126258985
3.5263-3.60290.36051500.3153285992
3.6029-3.68670.37111440.3097302796
3.6867-3.77890.34461380.3009299598
3.7789-3.8810.35081600.2811305598
3.881-3.99510.33671600.2747307398
3.9951-4.1240.37351320.2574299097
4.124-4.27130.29071530.2451304496
4.2713-4.44230.33531170.2257294895
4.4423-4.64430.24311380.2066293693
4.6443-4.88890.24061340.1874287592
4.8889-5.19490.25451430.189294394
5.1949-5.59550.25121680.1953304396
5.5955-6.15770.25611260.2053310697
6.1577-7.04650.30711470.2165316399
7.0465-8.86940.24631610.1959306996
8.8694-49.3190.19811570.1905315994

+
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