[English] 日本語
Yorodumi
- PDB-6lhg: Crystal structure of chicken cCD8aa/pBF2*04:01 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lhg
TitleCrystal structure of chicken cCD8aa/pBF2*04:01
Components
  • Beta-2-microglobulin
  • CD8 alpha chain
  • IE8 peptide
  • MHC class I alpha chain 2
KeywordsIMMUNE SYSTEM / chicken / complex / BF2*04:01
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 / adaptive immune response / intracellular iron ion homeostasis / learning or memory / immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular region / plasma membrane / cytosol
Similarity search - Function
CD8 alpha subunit / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein ...CD8 alpha subunit / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
MHC class I alpha chain 2 / Beta-2-microglobulin / T-cell surface glycoprotein CD8 alpha chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiu, Y.J. / Xia, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31572493 China
National Natural Science Foundation of China (NSFC)31972683 China
CitationJournal: Front Immunol / Year: 2020
Title: The Combination of CD8 alpha alpha and Peptide-MHC-I in a Face-to-Face Mode Promotes Chicken gamma delta T Cells Response.
Authors: Liu, Y. / Chen, R. / Liang, R. / Sun, B. / Wu, Y. / Zhang, L. / Kaufman, J. / Xia, C.
History
DepositionDec 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: 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 22, 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 1.3Oct 16, 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: IE8 peptide
G: CD8 alpha chain
H: CD8 alpha chain
D: MHC class I alpha chain 2
E: Beta-2-microglobulin
F: IE8 peptide
I: CD8 alpha chain
J: CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)141,10010
Polymers141,10010
Non-polymers00
Water79344
1
A: MHC class I alpha chain 2
B: Beta-2-microglobulin
C: IE8 peptide
G: CD8 alpha chain
H: CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)70,5505
Polymers70,5505
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class I alpha chain 2
E: Beta-2-microglobulin
F: IE8 peptide
I: CD8 alpha chain
J: CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)70,5505
Polymers70,5505
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.576, 90.817, 94.874
Angle α, β, γ (deg.)90.000, 98.614, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein MHC class I alpha chain 2 / BF2*04:01 / MHC class I glycoprotein / MHC class I molecule


Mass: 31445.982 Da / Num. of mol.: 2 / Mutation: D265E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B-FIV, BF2 / Production host: Escherichia coli (E. coli) / References: UniProt: O46790
#2: Protein Beta-2-microglobulin


Mass: 10915.230 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 IE8 peptide


Mass: 1010.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli)
#4: Protein
CD8 alpha chain


Mass: 13589.300 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6QR64
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M Bis-tris pH 6.5, 25% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 37579 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 14.14
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.613 / Num. unique obs: 163307

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E0R, 1CD8

4e0r

1cd8


Resolution: 2.8→29.869 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.891 / SU B: 0.01 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.377 / ESU R Free: 0.431
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2881 1874 4.995 %
Rwork0.2519 --
all0.254 --
obs-37516 99.602 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 80.574 Å2
Baniso -1Baniso -2Baniso -3
1-0.532 Å2-0 Å2-3.012 Å2
2--2.446 Å2-0 Å2
3----1.974 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9740 0 0 44 9784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8720.4091220.3632582X-RAY DIFFRACTION99.0476
2.872-2.950.3261310.3322547X-RAY DIFFRACTION99.9627
2.95-3.0350.3951320.3192473X-RAY DIFFRACTION99.885
3.035-3.1270.3591240.312415X-RAY DIFFRACTION99.882
3.127-3.2280.3361180.2882322X-RAY DIFFRACTION99.959
3.228-3.340.2981300.2842242X-RAY DIFFRACTION99.8737
3.34-3.4650.2951020.272197X-RAY DIFFRACTION99.9565
3.465-3.6040.2961210.2592078X-RAY DIFFRACTION99.9091
3.604-3.7620.3291070.2542033X-RAY DIFFRACTION99.9533
3.762-3.9430.294960.2491926X-RAY DIFFRACTION99.9012
3.943-4.1520.324930.2471850X-RAY DIFFRACTION99.8458
4.152-4.3990.275900.2161739X-RAY DIFFRACTION99.8362
4.399-4.6950.2211100.2161614X-RAY DIFFRACTION99.5956
4.695-5.0610.272820.2171545X-RAY DIFFRACTION99.7548
5.061-5.5280.227660.2321397X-RAY DIFFRACTION99.3886
5.528-6.1550.271670.2541287X-RAY DIFFRACTION99.3397
6.155-7.0570.299690.2631132X-RAY DIFFRACTION99.6681
7.057-8.5260.278510.217981X-RAY DIFFRACTION99.6139
8.526-11.5990.191370.206787X-RAY DIFFRACTION99.0385
11.599-29.80.3260.25495X-RAY DIFFRACTION97.9323

+
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