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- PDB-6lhf: Crystal structure of chicken cCD8aa/pBF2*15:01 -

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Basic information

Entry
Database: PDB / ID: 6lhf
TitleCrystal structure of chicken cCD8aa/pBF2*15:01
Components
  • Beta-2-microglobulin
  • CD8 alpha chain
  • MHC class I
  • RY0808 peptide
KeywordsIMMUNE SYSTEM / chicken / complex / BF2*15:01
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
Beta-2-microglobulin / T-cell surface glycoprotein CD8 alpha chain / MHC class I
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
B: Beta-2-microglobulin
C: RY0808 peptide
G: CD8 alpha chain
H: CD8 alpha chain
D: MHC class I
E: Beta-2-microglobulin
F: RY0808 peptide
I: CD8 alpha chain
J: CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)137,18710
Polymers137,18710
Non-polymers00
Water1,946108
1
A: MHC class I
B: Beta-2-microglobulin
C: RY0808 peptide
G: CD8 alpha chain
H: CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)68,5935
Polymers68,5935
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MHC class I
E: Beta-2-microglobulin
F: RY0808 peptide
I: CD8 alpha chain
J: CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)68,5935
Polymers68,5935
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.340, 66.735, 103.949
Angle α, β, γ (deg.)84.595, 82.041, 67.506
Int Tables number1
Space group name H-MP1

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Components

#1: Protein MHC class I / BF2*15:01 / MHC class I alpha chain 2 / MHC class I molecule


Mass: 30657.658 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: Q9GIP6
#2: Protein Beta-2-microglobulin / beta2m


Mass: 10800.142 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 RY0808 peptide


Mass: 1126.205 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: 13004.692 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.: 108 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium chloride, 25% (w/v) polyethylene glycol 3,350,0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97972 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97972 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 36586 / % possible obs: 95.8 % / Redundancy: 3 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.587
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.516 / Num. unique obs: 108500 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E0R

4e0r


Resolution: 2.7→29.893 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.862 / SU B: 0.011 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.394 / ESU R Free: 0.465
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.299 1662 5.024 %
Rwork0.2533 --
all0.256 --
obs-33078 95.458 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.453 Å2
Baniso -1Baniso -2Baniso -3
1--3.194 Å22.343 Å22.222 Å2
2--3.484 Å23.917 Å2
3---0.977 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9656 0 0 108 9764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.3861420.3342346X-RAY DIFFRACTION97.8757
2.77-2.8450.3431300.322281X-RAY DIFFRACTION98.2478
2.845-2.9260.3461090.2992270X-RAY DIFFRACTION98.0223
2.926-3.0160.37980.2872226X-RAY DIFFRACTION98.5163
3.016-3.1130.3221040.2842094X-RAY DIFFRACTION98.1688
3.113-3.2220.3471110.272096X-RAY DIFFRACTION98.3512
3.222-3.3420.3411230.261932X-RAY DIFFRACTION97.8106
3.342-3.4760.277790.2441914X-RAY DIFFRACTION97.5049
3.476-3.6290.313790.2371826X-RAY DIFFRACTION97.2435
3.629-3.8030.285970.2291697X-RAY DIFFRACTION96.8683
3.803-4.0050.274760.2381627X-RAY DIFFRACTION94.8746
4.005-4.2430.281900.2241505X-RAY DIFFRACTION93.2203
4.243-4.530.266640.2221328X-RAY DIFFRACTION88.6624
4.53-4.8840.244780.2111229X-RAY DIFFRACTION87.9542
4.884-5.3360.263580.2371167X-RAY DIFFRACTION90.3392
5.336-5.9420.289620.2691092X-RAY DIFFRACTION93.2149
5.942-6.8170.355630.279999X-RAY DIFFRACTION95.7619
6.817-8.2430.309370.257834X-RAY DIFFRACTION92.4628
8.243-11.2410.226440.223580X-RAY DIFFRACTION85.1296
11.241-29.80.247180.269373X-RAY DIFFRACTION86.6962

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