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- PDB-5wxc: Crystal Structure of HLA-A*2402 in complex with avian influenza A... -

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Basic information

Entry
Database: PDB / ID: 5wxc
TitleCrystal Structure of HLA-A*2402 in complex with avian influenza A(H7N9) virus-derived peptide H7-25 (data set 2)
Components
  • Beta-2-microglobulin
  • H7-25-F
  • HLA class I histocompatibility antigen, A-24 alpha chain
KeywordsIMMUNE SYSTEM / HLA-A*2402 / H1N1 / H5N1 / H1-25
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / viral budding from plasma membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion / 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 / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / 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 / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / Interferon gamma signaling / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / 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 / T cell receptor signaling pathway / late endosome membrane / 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 / structural constituent of virion / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / immune response / defense response to Gram-positive bacterium / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / cell surface / endoplasmic reticulum
Similarity search - Function
Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / MHC class I, alpha chain, C-terminal ...Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Matrix protein 1 / 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)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.295 Å
AuthorsZhao, M. / Liu, K. / Chai, Y. / Qi, J. / Liu, J. / Gao, G.F.
CitationJournal: Mbio / Year: 2018
Title: Heterosubtypic Protections against Human-Infecting Avian Influenza Viruses Correlate to Biased Cross-T-Cell Responses.
Authors: Zhao, M. / Liu, K. / Luo, J. / Tan, S. / Quan, C. / Zhang, S. / Chai, Y. / Qi, J. / Li, Y. / Bi, Y. / Xiao, H. / Wong, G. / Zhou, J. / Jiang, T. / Liu, W. / Yu, H. / Yan, J. / Liu, Y. / Shu, ...Authors: Zhao, M. / Liu, K. / Luo, J. / Tan, S. / Quan, C. / Zhang, S. / Chai, Y. / Qi, J. / Li, Y. / Bi, Y. / Xiao, H. / Wong, G. / Zhou, J. / Jiang, T. / Liu, W. / Yu, H. / Yan, J. / Liu, Y. / Shu, Y. / Wu, G. / Wu, A. / Gao, G.F. / Liu, W.J.
History
DepositionJan 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 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
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: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, A-24 alpha chain
D: Beta-2-microglobulin
E: H7-25-F
F: H7-25-F


Theoretical massNumber of molelcules
Total (without water)89,6646
Polymers89,6646
Non-polymers00
Water6,395355
1
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
E: H7-25-F


Theoretical massNumber of molelcules
Total (without water)44,8323
Polymers44,8323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-21 kcal/mol
Surface area18580 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, A-24 alpha chain
D: Beta-2-microglobulin
F: H7-25-F


Theoretical massNumber of molelcules
Total (without water)44,8323
Polymers44,8323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-23 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.373, 67.292, 88.346
Angle α, β, γ (deg.)90.00, 98.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, A-24 alpha chain / HLA-A*2402 / 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: 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 (E. coli) / References: UniProt: P05534, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / hB2m


Mass: 11819.238 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 H7-25-F


Mass: 1460.825 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (A/chicken/China/028/2014(H7N9))
References: UniProt: A0A0X9JHC1*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: SDMS / Detector: PIXEL / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.295→50 Å / Num. obs: 42274 / % possible obs: 99.14 % / Redundancy: 4.5 % / Net I/σ(I): 18.155

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
CNSdata reduction
CNSdata scaling
CNSphasing
RefinementResolution: 2.295→30.824 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.17
RfactorNum. reflection% reflection
Rfree0.224 1993 4.73 %
Rwork0.177 --
obs0.1791 42131 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.295→30.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6213 0 0 355 6568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066385
X-RAY DIFFRACTIONf_angle_d0.8558647
X-RAY DIFFRACTIONf_dihedral_angle_d25.8462375
X-RAY DIFFRACTIONf_chiral_restr0.053879
X-RAY DIFFRACTIONf_plane_restr0.0061131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.295-2.35240.31931340.23562560X-RAY DIFFRACTION90
2.3524-2.4160.30111470.21442883X-RAY DIFFRACTION99
2.416-2.48710.23871440.21292823X-RAY DIFFRACTION100
2.4871-2.56730.32291390.2172886X-RAY DIFFRACTION100
2.5673-2.6590.2751560.20822868X-RAY DIFFRACTION100
2.659-2.76540.28281610.20472865X-RAY DIFFRACTION100
2.7654-2.89120.28481400.19692854X-RAY DIFFRACTION100
2.8912-3.04350.26381480.19352885X-RAY DIFFRACTION100
3.0435-3.2340.2391520.18942876X-RAY DIFFRACTION100
3.234-3.48330.22231320.18252900X-RAY DIFFRACTION100
3.4833-3.83330.19621160.16372942X-RAY DIFFRACTION100
3.8333-4.38660.17031120.14382922X-RAY DIFFRACTION100
4.3866-5.52150.16021550.14142912X-RAY DIFFRACTION100
5.5215-30.82690.19331570.16542962X-RAY DIFFRACTION100

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