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- PDB-5xov: Crystal structure of peptide-HLA-A24 bound to S19-2 V-delta/V-beta TCR -

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Basic information

Entry
Database: PDB / ID: 5xov
TitleCrystal structure of peptide-HLA-A24 bound to S19-2 V-delta/V-beta TCR
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HIV-1 Nef138-10 peptide
  • HLA class I histocompatibility antigen, A-24 alpha chain
  • V-beta chain of T cell receptor
  • V-delta chain of T cell receptor
KeywordsIMMUNE SYSTEM / antigen presentation
Function / homology
Function and homology information


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 / suppression by virus of host autophagy / activation of transmembrane receptor protein tyrosine kinase activity / host cell Golgi membrane / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...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 / suppression by virus of host autophagy / activation of transmembrane receptor protein tyrosine kinase activity / host cell Golgi membrane / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / 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 / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / virion component / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / endocytosis involved in viral entry into host cell / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / SH3 domain binding / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response
Similarity search - Function
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 ...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 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein Nef / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.684 Å
AuthorsShi, Y. / Qi, J. / Gao, G.F.
CitationJournal: J. Virol. / Year: 2017
Title: Conserved V delta 1 Binding Geometry in a Setting of Locus-Disparate pHLA Recognition by delta / alpha beta T Cell Receptors (TCRs): Insight into Recognition of HIV Peptides by TCRs.
Authors: Shi, Y. / Kawana-Tachikawa, A. / Gao, F. / Qi, J. / Liu, C. / Gao, J. / Cheng, H. / Ueno, T. / Iwamoto, A. / Gao, G.F.
History
DepositionMay 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Nov 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

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: HIV-1 Nef138-10 peptide
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: HIV-1 Nef138-10 peptide
I: V-delta chain of T cell receptor
J: V-beta chain of T cell receptor
G: V-delta chain of T cell receptor
H: V-beta chain of T cell receptor


Theoretical massNumber of molelcules
Total (without water)190,49710
Polymers190,49710
Non-polymers00
Water7,134396
1
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: HIV-1 Nef138-10 peptide
I: V-delta chain of T cell receptor
J: V-beta chain of T cell receptor


Theoretical massNumber of molelcules
Total (without water)95,2485
Polymers95,2485
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-62 kcal/mol
Surface area38320 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-24 alpha chain
E: Beta-2-microglobulin
F: HIV-1 Nef138-10 peptide
G: V-delta chain of T cell receptor
H: V-beta chain of T cell receptor


Theoretical massNumber of molelcules
Total (without water)95,2485
Polymers95,2485
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-61 kcal/mol
Surface area38280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.992, 73.789, 163.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules ADBEIGJH

#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 A24


Mass: 31551.889 Da / Num. of mol.: 2 / Fragment: UNP residues 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P05534, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61769
#4: Protein V-delta chain of T cell receptor


Mass: 23225.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#5: Protein V-beta chain of T cell receptor


Mass: 27301.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Protein/peptide / Non-polymers , 2 types, 398 molecules CF

#3: Protein/peptide HIV-1 Nef138-10 peptide


Mass: 1290.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P03407*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5%(v/v) Tacsimate pH 7.0, 0.1M HEPES, pH 7.3, 10%(w/v) polyethylene glycol monomethyl either 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 10, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 68358 / % possible obs: 99.8 % / Redundancy: 3.4 % / Net I/σ(I): 12.8
Reflection shellResolution: 2.68→2.78 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A9E, 2IAL

1a9e

2ial


Resolution: 2.684→37.999 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.78
RfactorNum. reflection% reflection
Rfree0.245 3459 5.06 %
Rwork0.2029 --
obs0.205 68316 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 30.36 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4395 Å20 Å20.6245 Å2
2--2.1425 Å2-0 Å2
3---1.297 Å2
Refinement stepCycle: LAST / Resolution: 2.684→37.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13416 0 0 396 13812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513792
X-RAY DIFFRACTIONf_angle_d0.87918706
X-RAY DIFFRACTIONf_dihedral_angle_d18.6024938
X-RAY DIFFRACTIONf_chiral_restr0.061968
X-RAY DIFFRACTIONf_plane_restr0.0042434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.684-2.72080.34951320.2782535X-RAY DIFFRACTION98
2.7208-2.75960.32241280.28962598X-RAY DIFFRACTION100
2.7596-2.80080.35411390.26972549X-RAY DIFFRACTION100
2.8008-2.84460.31471370.25992588X-RAY DIFFRACTION100
2.8446-2.89120.28341220.25892560X-RAY DIFFRACTION100
2.8912-2.9410.34181400.2672631X-RAY DIFFRACTION100
2.941-2.99450.32961480.24462564X-RAY DIFFRACTION100
2.9945-3.05210.25761310.23642573X-RAY DIFFRACTION100
3.0521-3.11430.2981400.23762586X-RAY DIFFRACTION100
3.1143-3.1820.25241430.23592566X-RAY DIFFRACTION100
3.182-3.2560.29131180.23182587X-RAY DIFFRACTION100
3.256-3.33740.31841520.22672612X-RAY DIFFRACTION100
3.3374-3.42760.26311470.2172573X-RAY DIFFRACTION100
3.4276-3.52830.2911340.22662601X-RAY DIFFRACTION100
3.5283-3.64210.2961290.21452579X-RAY DIFFRACTION100
3.6421-3.77220.22531290.21052616X-RAY DIFFRACTION100
3.7722-3.92310.23791450.18562610X-RAY DIFFRACTION100
3.9231-4.10140.2261240.17952601X-RAY DIFFRACTION100
4.1014-4.31740.18121310.15882608X-RAY DIFFRACTION100
4.3174-4.58750.16281360.13852637X-RAY DIFFRACTION100
4.5875-4.9410.2061580.14032570X-RAY DIFFRACTION100
4.941-5.43690.1551730.14462591X-RAY DIFFRACTION100
5.4369-6.22070.22571480.1672617X-RAY DIFFRACTION100
6.2207-7.82610.21151490.19242642X-RAY DIFFRACTION100
7.8261-38.00230.25451260.19152663X-RAY DIFFRACTION97

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