[English] 日本語
Yorodumi
- PDB-7wbg: BF2*1901/RY8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wbg
TitleBF2*1901/RY8
Components
  • ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR
  • Beta-2-microglobulin
  • MHC class I alpha chain 2
KeywordsIMMUNE SYSTEM / MHC I
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / cellular response to iron ion / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / cellular response to iron ion / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / 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 / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / positive regulation of cellular senescence / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular region / cytosol
Similarity search - Function
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 / : ...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
MHC class I alpha chain 2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesGallus gallus (chicken)
uncultured virus (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, W.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Immunol. / Year: 2023
Title: A Wider and Deeper Peptide-Binding Groove for the Class I Molecules from B15 Compared with B19 Chickens Correlates with Relative Resistance to Marek's Disease.
Authors: Han, L. / Wu, S. / Zhang, T. / Peng, W. / Zhao, M. / Yue, C. / Wen, W. / Cai, W. / Li, M. / Wallny, H.J. / Avila, D.W. / Mwangi, W. / Nair, V. / Ternette, N. / Guo, Y. / Zhao, Y. / Chai, Y. ...Authors: Han, L. / Wu, S. / Zhang, T. / Peng, W. / Zhao, M. / Yue, C. / Wen, W. / Cai, W. / Li, M. / Wallny, H.J. / Avila, D.W. / Mwangi, W. / Nair, V. / Ternette, N. / Guo, Y. / Zhao, Y. / Chai, Y. / Qi, J. / Liang, H. / Gao, G.F. / Kaufman, J. / Liu, W.J.
History
DepositionDec 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: 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 1.2Nov 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: MHC class I alpha chain 2
B: Beta-2-microglobulin
C: ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR
D: MHC class I alpha chain 2
E: Beta-2-microglobulin
F: ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR


Theoretical massNumber of molelcules
Total (without water)85,9816
Polymers85,9816
Non-polymers00
Water10,611589
1
A: MHC class I alpha chain 2
B: Beta-2-microglobulin
C: ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR


Theoretical massNumber of molelcules
Total (without water)42,9913
Polymers42,9913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-13 kcal/mol
Surface area17620 Å2
MethodPISA
2
D: MHC class I alpha chain 2
E: Beta-2-microglobulin
F: ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR


Theoretical massNumber of molelcules
Total (without water)42,9913
Polymers42,9913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-9 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.127, 85.025, 110.838
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein MHC class I alpha chain 2 / MHC class I molecule


Mass: 30801.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: BF2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0ZXM5
#2: Protein Beta-2-microglobulin


Mass: 11062.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P21611
#3: Protein/peptide ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR


Mass: 1126.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Potassium bromide and 30% w/v Polyethylene glycol monomethyl ether 2,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 49775 / % possible obs: 98.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 23.42 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.142 / Num. unique obs: 4913

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHASER1.13_2998phasing
Cootmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YEZ

2yez


Resolution: 2→33.4 Å / SU ML: 0.202 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.7077 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2358 2508 5.04 %
Rwork0.183 47267 -
obs0.1856 49775 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.36 Å2
Refinement stepCycle: LAST / Resolution: 2→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 0 589 6583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00756170
X-RAY DIFFRACTIONf_angle_d0.90658388
X-RAY DIFFRACTIONf_chiral_restr0.0548844
X-RAY DIFFRACTIONf_plane_restr0.00571106
X-RAY DIFFRACTIONf_dihedral_angle_d6.88373596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.26631350.192551X-RAY DIFFRACTION97.57
2.04-2.080.22061500.1822638X-RAY DIFFRACTION100
2.08-2.120.28481600.18282620X-RAY DIFFRACTION100
2.12-2.170.2451350.182660X-RAY DIFFRACTION100
2.17-2.230.26391280.17692653X-RAY DIFFRACTION100
2.23-2.290.26151490.17632641X-RAY DIFFRACTION100
2.29-2.350.24021350.18742656X-RAY DIFFRACTION99.96
2.35-2.430.24461300.19092651X-RAY DIFFRACTION100
2.43-2.520.21241540.18142648X-RAY DIFFRACTION100
2.52-2.620.26271310.18942662X-RAY DIFFRACTION100
2.62-2.740.251440.19642665X-RAY DIFFRACTION99.93
2.74-2.880.25931280.20152678X-RAY DIFFRACTION99.96
2.88-3.060.26151330.19892681X-RAY DIFFRACTION99.79
3.06-3.30.22961420.18782655X-RAY DIFFRACTION98.76
3.3-3.630.23421680.18562560X-RAY DIFFRACTION96.19
3.63-4.150.21611210.1682574X-RAY DIFFRACTION94.2
4.15-5.230.20541320.16312394X-RAY DIFFRACTION87.16
5.23-33.40.21531330.18112680X-RAY DIFFRACTION93.27

+
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