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- PDB-7f4w: Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope pep4 -

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Basic information

Entry
Database: PDB / ID: 7f4w
TitleComplex structure of HLA2402 with recognizing SARS-CoV-2 epitope pep4
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • SARS-CoV-2 T-cell Epitope pep4
KeywordsIMMUNE SYSTEM / MHC / HLA / SARS-CoV-2 / epitope
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / cellular response to iron ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / 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. / Immunoglobulin C-Type / Immunoglobulin C1-set ...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: 2.9 Å
AuthorsDeng, S. / Jin, T.
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
DepositionJun 21, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: MHC class I antigen
D: Beta-2-microglobulin
E: SARS-CoV-2 T-cell Epitope pep4
F: SARS-CoV-2 T-cell Epitope pep4


Theoretical massNumber of molelcules
Total (without water)97,5946
Polymers97,5946
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
E: SARS-CoV-2 T-cell Epitope pep4


Theoretical massNumber of molelcules
Total (without water)48,7973
Polymers48,7973
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-24 kcal/mol
Surface area18980 Å2
MethodPISA
2
C: MHC class I antigen
D: Beta-2-microglobulin
F: SARS-CoV-2 T-cell Epitope pep4


Theoretical massNumber of molelcules
Total (without water)48,7973
Polymers48,7973
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-21 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.440, 135.600, 153.330
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: 35437.070 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: D9UAY1
#2: Protein Beta-2-microglobulin


Mass: 12093.574 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 pep4


Mass: 1266.425 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
Has ligand of interestN

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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: 2.62 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 0.1 M HEPES pH8.1 22%(v/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.9→47.83 Å / Num. obs: 22639 / % possible obs: 99.5 % / Redundancy: 12.1 % / Biso Wilson estimate: 59.61 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.34 / Rrim(I) all: 0.355 / Net I/σ(I): 13.39
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 1.65 / Num. unique obs: 1659 / CC1/2: 0.762 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BCK

2bck


Resolution: 2.9→47.83 Å / SU ML: 0.4006 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2982 1131 5 %
Rwork0.2438 21491 -
obs0.2466 22622 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.75 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6388 0 6 0 6394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00966565
X-RAY DIFFRACTIONf_angle_d1.1118891
X-RAY DIFFRACTIONf_chiral_restr0.058900
X-RAY DIFFRACTIONf_plane_restr0.01011170
X-RAY DIFFRACTIONf_dihedral_angle_d6.9005878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.36861390.34012622X-RAY DIFFRACTION99.17
3.03-3.190.37171400.31142660X-RAY DIFFRACTION99.89
3.19-3.390.36431400.30282666X-RAY DIFFRACTION99.89
3.39-3.650.37111380.2872640X-RAY DIFFRACTION99.21
3.65-4.020.32131390.26652639X-RAY DIFFRACTION98.55
4.02-4.60.23181400.21842660X-RAY DIFFRACTION99.04
4.6-5.80.2941440.20152735X-RAY DIFFRACTION99.76
5.8-47.830.24151510.19812869X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: 11.5553652787 Å / Origin y: 1.99511334033 Å / Origin z: -35.40789464 Å
111213212223313233
T0.326196628734 Å20.0866392189978 Å20.0301693168275 Å2-0.340872599445 Å20.0162856451213 Å2--0.398386444009 Å2
L0.478451145502 °20.275959507297 °2-0.115817082645 °2-0.304778358575 °2-0.305422318339 °2--0.569723529193 °2
S-0.00655062283963 Å °-0.0407086780033 Å °0.109364068551 Å °0.0265621849385 Å °0.0164391163786 Å °0.0855227863273 Å °0.0123504931985 Å °0.0258491211995 Å °0.000927855570072 Å °
Refinement TLS groupSelection details: all

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