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- PDB-7ejm: Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-22... -

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Basic information

Entry
Database: PDB / ID: 7ejm
TitleComplex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-229E) spike protein
Components
  • 9-mer peptide from the HCoV spike protein
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA-A*2402 / MHC CLASS I / coronavirus
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-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 / : ...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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Shirouzu, M.
CitationJournal: Commun Biol / Year: 2021
Title: Identification of TCR repertoires in functionally competent cytotoxic T cells cross-reactive to SARS-CoV-2.
Authors: Shimizu, K. / Iyoda, T. / Sanpei, A. / Nakazato, H. / Okada, M. / Ueda, S. / Kato-Murayama, M. / Murayama, K. / Shirouzu, M. / Harada, N. / Hidaka, M. / Fujii, S.I.
History
DepositionApr 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: 9-mer peptide from the HCoV spike protein


Theoretical massNumber of molelcules
Total (without water)45,6183
Polymers45,6183
Non-polymers00
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-22 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.946, 85.586, 91.091
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MHC class I antigen


Mass: 32071.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Details (production host): Cell-free protein synthesis / Production host: Escherichia coli (E. coli) / References: UniProt: A0A411J078
#2: Protein Beta-2-microglobulin


Mass: 12267.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Details (production host): Cell-free protein synthesis / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide 9-mer peptide from the HCoV spike protein


Mass: 1279.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human coronavirus 229E
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Na citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→45.95 Å / Num. obs: 111576 / % possible obs: 99.99 % / Redundancy: 7.7 % / Biso Wilson estimate: 26.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.5
Reflection shellResolution: 1.71→1.77 Å / Num. unique obs: 11121 / CC1/2: 0.492

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F7M

4f7m


Resolution: 1.71→45.95 Å / SU ML: 0.2726 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.6121 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.221 2793 4.83 %
Rwork0.1915 55045 -
obs0.1929 57838 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.64 Å2
Refinement stepCycle: LAST / Resolution: 1.71→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 0 491 3655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693257
X-RAY DIFFRACTIONf_angle_d0.82574420
X-RAY DIFFRACTIONf_chiral_restr0.0558445
X-RAY DIFFRACTIONf_plane_restr0.0051579
X-RAY DIFFRACTIONf_dihedral_angle_d3.04541916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.740.41071750.38692682X-RAY DIFFRACTION99.44
1.74-1.770.35851400.35262668X-RAY DIFFRACTION99.96
1.77-1.810.34521480.33142701X-RAY DIFFRACTION99.93
1.81-1.840.3221350.28552728X-RAY DIFFRACTION99.97
1.84-1.880.30481360.26142750X-RAY DIFFRACTION100
1.88-1.930.2571390.23622699X-RAY DIFFRACTION100
1.93-1.980.25011340.22652743X-RAY DIFFRACTION100
1.98-2.030.23141530.2092711X-RAY DIFFRACTION99.97
2.03-2.090.2421360.20542726X-RAY DIFFRACTION100
2.09-2.160.23291370.1962720X-RAY DIFFRACTION100
2.16-2.230.20511250.19232781X-RAY DIFFRACTION100
2.23-2.320.22051150.18672741X-RAY DIFFRACTION99.96
2.32-2.430.2751230.19952779X-RAY DIFFRACTION100
2.43-2.560.20641340.19962750X-RAY DIFFRACTION100
2.56-2.720.26011390.19792757X-RAY DIFFRACTION100
2.72-2.930.24121350.20012772X-RAY DIFFRACTION100
2.93-3.220.19811650.19062749X-RAY DIFFRACTION100
3.22-3.690.1991250.16712810X-RAY DIFFRACTION100
3.69-4.650.18391450.15112820X-RAY DIFFRACTION100
4.65-45.950.18211540.16582958X-RAY DIFFRACTION99.81

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