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- PDB-7eu2: Complex structure of HLA0201 with recognizing SARS-CoV-2 epitope S1 -

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Basic information

Entry
Database: PDB / ID: 7eu2
TitleComplex structure of HLA0201 with recognizing SARS-CoV-2 epitope S1
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • SARS-CoV-2 T-cell Epitope S1
KeywordsIMMUNE SYSTEM / MHC / HLA / SARS-CoV-2 / epitope
Function / homology
Function and homology information


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 / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion ...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 / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal 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, C-terminal / MHC_I C-terminus / 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, alpha chain, C-terminal / MHC_I C-terminus / 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: 2.8 Å
AuthorsDeng, S. / Jin, T.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29030104 China
CitationJournal: Cell Rep / Year: 2021
Title: Profiling CD8 + T cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants.
Authors: Zhang, H. / Deng, S. / Ren, L. / Zheng, P. / Hu, X. / Jin, T. / Tan, X.
History
DepositionMay 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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: SARS-CoV-2 T-cell Epitope S1
D: MHC class I antigen
E: Beta-2-microglobulin
F: SARS-CoV-2 T-cell Epitope S1


Theoretical massNumber of molelcules
Total (without water)97,9556
Polymers97,9556
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: SARS-CoV-2 T-cell Epitope S1


Theoretical massNumber of molelcules
Total (without water)48,9773
Polymers48,9773
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-21 kcal/mol
Surface area19570 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: SARS-CoV-2 T-cell Epitope S1


Theoretical massNumber of molelcules
Total (without water)48,9773
Polymers48,9773
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-19 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.490, 103.340, 128.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein MHC class I antigen


Mass: 35610.270 Da / Num. of mol.: 2
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: A0A5H2UU57
#2: Protein Beta-2-microglobulin


Mass: 12237.704 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 SARS-CoV-2 T-cell Epitope S1


Mass: 1129.306 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 26% PEG 4000, 0.2 M Sodium acetate, and 0.1 M Tris-HCl pH9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→43.134 Å / Num. obs: 23705 / % possible obs: 99.8 % / Redundancy: 7.75 % / CC1/2: 0.995 / Rrim(I) all: 0.219 / Net I/σ(I): 10.73
Reflection shellResolution: 2.8→2.87 Å / Mean I/σ(I) obs: 1.69 / Num. unique obs: 1720 / CC1/2: 0.654 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HHN

5hhn


Resolution: 2.8→43.134 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 1186 5.01 %
Rwork0.2312 --
obs0.233 23690 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→43.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6379 0 0 0 6379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046564
X-RAY DIFFRACTIONf_angle_d0.8798904
X-RAY DIFFRACTIONf_dihedral_angle_d12.8483856
X-RAY DIFFRACTIONf_chiral_restr0.048904
X-RAY DIFFRACTIONf_plane_restr0.0041159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.92760.36271450.33512754X-RAY DIFFRACTION100
2.9276-3.08190.34041450.30912763X-RAY DIFFRACTION100
3.0819-3.27490.31361460.29262759X-RAY DIFFRACTION100
3.2749-3.52770.31371470.26322807X-RAY DIFFRACTION100
3.5277-3.88250.2651480.23272789X-RAY DIFFRACTION100
3.8825-4.44380.27261470.20972819X-RAY DIFFRACTION100
4.4438-5.59680.21291510.1842843X-RAY DIFFRACTION100
5.5968-43.1340.22531570.20362970X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 3.8945 Å / Origin y: -38.8168 Å / Origin z: 14.7295 Å
111213212223313233
T0.3489 Å20.0621 Å20.0114 Å2-0.3638 Å20.0008 Å2--0.3198 Å2
L1.0874 °20.0218 °2-0.3089 °2-1.0176 °2-0.4446 °2--1.0941 °2
S0.0715 Å °0.1568 Å °0.1113 Å °-0.172 Å °-0.0835 Å °-0.0985 Å °0.001 Å °-0.0324 Å °0.008 Å °
Refinement TLS groupSelection details: all

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