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- PDB-3qzw: Plasticity of human CD8 binding to peptide-HLA-A*2402 -

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Basic information

Entry
Database: PDB / ID: 3qzw
TitlePlasticity of human CD8 binding to peptide-HLA-A*2402
Components
  • 10-mer peptide from Protein Nef
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-24 alpha chain
  • T-cell surface glycoprotein CD8 alpha chain
KeywordsIMMUNE SYSTEM / Immunoglobulin family / coreceptor
Function / homology
Function and homology information


cytotoxic T cell differentiation / MHC class I protein complex binding / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / T cell mediated immunity / symbiont-mediated suppression of host autophagy / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation ...cytotoxic T cell differentiation / MHC class I protein complex binding / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / T cell mediated immunity / symbiont-mediated suppression of host autophagy / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex / antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / host cell Golgi membrane / endoplasmic reticulum exit site / MHC class I protein binding / TAP binding / plasma membrane raft / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / coreceptor activity / T cell receptor binding / cell surface receptor protein tyrosine kinase signaling pathway / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / T cell activation / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / SH3 domain binding / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / virion component / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of type II interferon production / recycling endosome membrane / Interferon gamma signaling / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / T cell receptor signaling pathway / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / cell surface receptor signaling pathway / signaling receptor complex / defense response to Gram-positive bacterium
Similarity search - Function
CD8 alpha subunit / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 ...CD8 alpha subunit / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD8 alpha chain / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Protein Nef
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 Å
AuthorsShi, Y. / Qi, J. / Gao, G.F.
CitationJournal: Mol.Immunol. / Year: 2011
Title: Plasticity of human CD8alpha alpha binding to peptide-HLA-A*2402
Authors: Shi, Y. / Qi, J. / Iwamoto, A. / Gao, G.F.
History
DepositionMar 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: 10-mer peptide from Protein Nef
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: 10-mer peptide from Protein Nef
G: T-cell surface glycoprotein CD8 alpha chain
H: T-cell surface glycoprotein CD8 alpha chain
I: T-cell surface glycoprotein CD8 alpha chain
J: T-cell surface glycoprotein CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)140,84210
Polymers140,84210
Non-polymers00
Water2,954164
1
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: 10-mer peptide from Protein Nef
G: T-cell surface glycoprotein CD8 alpha chain
H: T-cell surface glycoprotein CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)70,4215
Polymers70,4215
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: 10-mer peptide from Protein Nef
I: T-cell surface glycoprotein CD8 alpha chain
J: T-cell surface glycoprotein CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)70,4215
Polymers70,4215
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.239, 67.019, 101.144
Angle α, β, γ (deg.)73.71, 71.84, 81.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein HLA class I histocompatibility antigen, A-24 alpha chain / Aw-24 / HLA class I histocompatibility antigen / A-9 alpha chain / MHC class I antigen A*24


Mass: 31551.889 Da / Num. of mol.: 2 / Fragment: extracellular domains, alpha1, alpha2, alpha3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P05534, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide 10-mer peptide from Protein Nef


Mass: 1290.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PEPTIDE WAS CHEMICALLY SYNTHESIZED. / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YYU8
#4: Protein
T-cell surface glycoprotein CD8 alpha chain / T-lymphocyte differentiation antigen T8/Leu-2


Mass: 12849.552 Da / Num. of mol.: 4 / Fragment: ectodomain (UNP residues 22-135)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD8A, MAL / Production host: Escherichia coli (E. coli) / References: UniProt: P01732
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES monohydrate, pH 6.5, 12% w/v PEG 20000, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 20, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.798→50 Å / Num. obs: 38431 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.9 Å / % possible all: 95.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.798→31.613 Å / SU ML: 0.39 / σ(F): 1.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 1926 5.01 %
Rwork0.2018 --
obs0.2048 38408 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.129 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.1583 Å21.1003 Å211.0045 Å2
2--4.2984 Å20.0721 Å2
3----17.4567 Å2
Refinement stepCycle: LAST / Resolution: 2.798→31.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9922 0 0 164 10086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510208
X-RAY DIFFRACTIONf_angle_d0.82313824
X-RAY DIFFRACTIONf_dihedral_angle_d16.5743672
X-RAY DIFFRACTIONf_chiral_restr0.0571430
X-RAY DIFFRACTIONf_plane_restr0.0031804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7976-2.86750.3381220.27692433X-RAY DIFFRACTION92
2.8675-2.9450.37531220.26762585X-RAY DIFFRACTION98
2.945-3.03160.37071210.25932638X-RAY DIFFRACTION98
3.0316-3.12940.34251330.26232604X-RAY DIFFRACTION99
3.1294-3.24110.33581450.22652607X-RAY DIFFRACTION98
3.2411-3.37080.2791360.22612652X-RAY DIFFRACTION99
3.3708-3.5240.27151310.20482596X-RAY DIFFRACTION99
3.524-3.70950.24221320.19572645X-RAY DIFFRACTION99
3.7095-3.94150.2451460.18732613X-RAY DIFFRACTION99
3.9415-4.24520.2131530.17092594X-RAY DIFFRACTION99
4.2452-4.67120.20811570.14972616X-RAY DIFFRACTION99
4.6712-5.34430.22681360.15422627X-RAY DIFFRACTION99
5.3443-6.72250.23021480.18852660X-RAY DIFFRACTION100
6.7225-31.61510.21141440.17552612X-RAY DIFFRACTION99

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