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- PDB-8z08: The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 ... -

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Basic information

Entry
Database: PDB / ID: 8z08
TitleThe structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYQYRLF(BA.2.12.1)
Components
  • ASN-TYR-ASN-TYR-GLN-TYR-ARG-LEU-PHE
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Complex / Peptide presentation
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / 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 iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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. ...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
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsZhang, J.N. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat.Immunol. / Year: 2025
Title: T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots.
Authors: Tian, J. / Shang, B. / Zhang, J. / Guo, Y. / Li, M. / Hu, Y. / Bai, D. / She, J. / Han, Y. / Guo, P. / Huang, M. / Wang, Y. / Liu, M. / Zhang, J. / Ye, B. / Guo, Y. / Yang, M. / Lin, Y. / ...Authors: Tian, J. / Shang, B. / Zhang, J. / Guo, Y. / Li, M. / Hu, Y. / Bai, D. / She, J. / Han, Y. / Guo, P. / Huang, M. / Wang, Y. / Liu, M. / Zhang, J. / Ye, B. / Guo, Y. / Yang, M. / Lin, Y. / Zhang, T. / Sun, X. / Yuan, X. / Zhang, D. / Xu, Z. / Chai, Y. / Qi, J. / Liu, K. / Tan, S. / Zhao, Y. / Zhou, J. / Song, R. / Gao, G.F. / Liu, J.
History
DepositionApr 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Structure summary / Category: citation / citation_author / struct
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 / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: MHC class I antigen
D: Beta-2-microglobulin
F: ASN-TYR-ASN-TYR-GLN-TYR-ARG-LEU-PHE


Theoretical massNumber of molelcules
Total (without water)44,7133
Polymers44,7133
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-17 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.140, 65.860, 49.990
Angle α, β, γ (deg.)90.000, 90.380, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-375-

HOH

21C-487-

HOH

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Components

#1: Protein MHC class I antigen / HLA class I heavy chain


Mass: 31551.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A143Y4R2
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
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 ASN-TYR-ASN-TYR-GLN-TYR-ARG-LEU-PHE


Mass: 1281.396 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-Tris, 20%w/v Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.01→40.54 Å / Num. obs: 34520 / % possible obs: 98.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.39 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.2
Reflection shellResolution: 2.01→2.06 Å / Rmerge(I) obs: 0.873 / Num. unique obs: 34520

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F4W

7f4w


Resolution: 2.01→27.5 Å / SU ML: 0.234 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4661
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 1694 4.91 %
Rwork0.1841 32806 -
obs0.1865 34500 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.31 Å2
Refinement stepCycle: LAST / Resolution: 2.01→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 0 326 3477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073237
X-RAY DIFFRACTIONf_angle_d0.83984386
X-RAY DIFFRACTIONf_chiral_restr0.0497442
X-RAY DIFFRACTIONf_plane_restr0.0073579
X-RAY DIFFRACTIONf_dihedral_angle_d6.1416434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.070.31761420.2592676X-RAY DIFFRACTION96.44
2.07-2.140.30651150.23442724X-RAY DIFFRACTION97.26
2.14-2.210.26741440.2162673X-RAY DIFFRACTION97.47
2.21-2.30.26151480.21262715X-RAY DIFFRACTION97.58
2.3-2.410.28051380.20262719X-RAY DIFFRACTION98.14
2.41-2.530.25411440.19972719X-RAY DIFFRACTION98.12
2.53-2.690.25041400.19382712X-RAY DIFFRACTION97.97
2.69-2.90.21091520.19282745X-RAY DIFFRACTION98.5
2.9-3.190.24741410.18452749X-RAY DIFFRACTION98.7
3.19-3.650.21351330.17252762X-RAY DIFFRACTION98.4
3.65-4.590.21111540.15752796X-RAY DIFFRACTION99.23
4.6-27.50.19361430.16012816X-RAY DIFFRACTION98.34

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