[English] 日本語
Yorodumi
- PDB-7emc: Mooring Stone-Like Arg114 Pulls Diverse Bulged Peptides: First In... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7emc
TitleMooring Stone-Like Arg114 Pulls Diverse Bulged Peptides: First Insight into African Swine Fever Virus-Derived T Cell Epitopes Presented by Swine Major Histocompatibility Complex Class I
Components
  • ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL
  • Beta-2-microglobulin
  • Leucocyte antigen
KeywordsIMMUNE SYSTEM / MHC class I
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / positive regulation of T cell activation / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / immune response / lysosomal membrane / extracellular region
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Similarity search - Domain/homology
Leucocyte antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesSus scrofa (pig)
uncultured virus (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. ...Yue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. / Ba, L. / Chai, Y. / Qi, J. / Liu, P. / Qi, P. / Zhao, Y. / Li, Y. / Qiu, H.J. / Gao, G.F. / Gao, G. / Liu, W.J.
CitationJournal: J.Virol. / Year: 2022
Title: Mooring Stone-Like Arg 114 Pulls Diverse Bulged Peptides: First Insight into African Swine Fever Virus-Derived T Cell Epitopes Presented by Swine Major Histocompatibility Complex Class I.
Authors: Yue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. / Ba, L. / Chai, Y. / Qi, J. / Liu, P. / Qi, P. / Zhao, Y. / Li, Y. / Qiu, H.J. / Gao, ...Authors: Yue, C. / Xiang, W. / Huang, X. / Sun, Y. / Xiao, J. / Liu, K. / Sun, Z. / Qiao, P. / Li, H. / Gan, J. / Ba, L. / Chai, Y. / Qi, J. / Liu, P. / Qi, P. / Zhao, Y. / Li, Y. / Qiu, H.J. / Gao, G.F. / Gao, G. / Liu, W.J.
History
DepositionApr 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucocyte antigen
B: Beta-2-microglobulin
C: ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL
D: Leucocyte antigen
E: Beta-2-microglobulin
F: ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL
G: Leucocyte antigen
H: Beta-2-microglobulin
I: ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL


Theoretical massNumber of molelcules
Total (without water)133,7339
Polymers133,7339
Non-polymers00
Water25,5091416
1
A: Leucocyte antigen
B: Beta-2-microglobulin
C: ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL


Theoretical massNumber of molelcules
Total (without water)44,5783
Polymers44,5783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-13 kcal/mol
Surface area18850 Å2
MethodPISA
2
D: Leucocyte antigen
E: Beta-2-microglobulin
F: ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL


Theoretical massNumber of molelcules
Total (without water)44,5783
Polymers44,5783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-11 kcal/mol
Surface area19020 Å2
MethodPISA
3
G: Leucocyte antigen
H: Beta-2-microglobulin
I: ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL


Theoretical massNumber of molelcules
Total (without water)44,5783
Polymers44,5783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-12 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.534, 110.632, 136.228
Angle α, β, γ (deg.)90.000, 95.422, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Leucocyte antigen / MHC class I antigen


Mass: 31825.113 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: sla-, SLA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O19075
#2: Protein Beta-2-microglobulin / Lactollin


Mass: 11708.207 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q07717
#3: Protein/peptide ALA-THR-GLU-ILE-ARG-GLU-LEU-LEU-VAL


Mass: 1044.222 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1416 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M BIS-TRIS pH6.5,16%w/v polyethylene glycol 10000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 95001 / % possible obs: 98.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.92
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.219 / Num. unique obs: 95001

-
Processing

Software
NameVersionClassification
XDS1.13_2998data scaling
PHASERphasing
Cootmodel building
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ3

3qq3


Resolution: 1.9→45.21 Å / SU ML: 0.1832 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 25.7025 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.226 4738 5 %
Rwork0.1802 90067 -
obs0.1825 94805 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9372 0 0 1416 10788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00689637
X-RAY DIFFRACTIONf_angle_d0.835613096
X-RAY DIFFRACTIONf_chiral_restr0.05141336
X-RAY DIFFRACTIONf_plane_restr0.0051732
X-RAY DIFFRACTIONf_dihedral_angle_d13.09926294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.29571310.22862860X-RAY DIFFRACTION94.23
1.92-1.940.26641360.20432977X-RAY DIFFRACTION97.01
1.94-1.970.24761420.18292988X-RAY DIFFRACTION96.99
1.97-1.990.23261650.17112976X-RAY DIFFRACTION97.21
1.99-2.020.23841500.1742961X-RAY DIFFRACTION97.46
2.02-2.040.22111620.18142935X-RAY DIFFRACTION97.39
2.04-2.070.23221690.17893031X-RAY DIFFRACTION97.44
2.07-2.10.26441560.18482936X-RAY DIFFRACTION97.45
2.1-2.140.25821490.1832978X-RAY DIFFRACTION97.48
2.14-2.170.25081530.18013014X-RAY DIFFRACTION97.96
2.17-2.210.22251560.17822967X-RAY DIFFRACTION97.65
2.21-2.250.20481700.18012969X-RAY DIFFRACTION97.82
2.25-2.290.23881600.17913008X-RAY DIFFRACTION97.96
2.29-2.340.22791610.18662974X-RAY DIFFRACTION98
2.34-2.390.22761560.18533015X-RAY DIFFRACTION98.11
2.39-2.450.25161620.18533062X-RAY DIFFRACTION98.41
2.45-2.510.23791420.18542975X-RAY DIFFRACTION98.55
2.51-2.580.22911720.18843019X-RAY DIFFRACTION98.67
2.58-2.650.24661600.1993005X-RAY DIFFRACTION98.81
2.65-2.740.24511910.18793020X-RAY DIFFRACTION98.71
2.74-2.830.22091610.19163000X-RAY DIFFRACTION98.94
2.83-2.950.22681700.18193069X-RAY DIFFRACTION98.99
2.95-3.080.2221840.18362958X-RAY DIFFRACTION98.99
3.08-3.240.23671650.18583062X-RAY DIFFRACTION99.17
3.24-3.450.23241530.17313069X-RAY DIFFRACTION98.96
3.45-3.710.19521570.16783013X-RAY DIFFRACTION99.03
3.71-4.090.19461590.16843066X-RAY DIFFRACTION98.93
4.09-4.680.18771450.15463038X-RAY DIFFRACTION98.73
4.68-5.890.21771480.16693104X-RAY DIFFRACTION98.97
5.89-45.210.22511530.20053018X-RAY DIFFRACTION96.41

+
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