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- PDB-6lhg: Crystal structure of chicken cCD8aa/pBF2*04:01 -

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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


cytotoxic T cell differentiation / 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 / T cell mediated immunity / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib ...cytotoxic T cell differentiation / 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 / T cell mediated immunity / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / 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 / Immunoglobulin V-set domain ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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