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- PDB-8rcv: Crystal structure of HLA B*13:01 in complex with SVLNDIFSRL, an 1... -

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Basic information

Entry
Database: PDB / ID: 8rcv
TitleCrystal structure of HLA B*13:01 in complex with SVLNDIFSRL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen B alpha chain
  • Spike protein S2'
KeywordsIMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-A11 / HLA-B*13:01 / SARS-CoV-2 / Spike
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway ...antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / intracellular iron ion homeostasis / structural constituent of virion / amyloid fibril formation / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / learning or memory / host cell surface receptor binding / immune response / Amyloid fiber formation / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / Neutrophil degranulation / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity
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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
HLA class I histocompatibility antigen B alpha chain / Spike glycoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAhn, Y.M. / Maddumage, J.C. / Szeto, C. / Gras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Curr Res Struct Biol / Year: 2024
Title: The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific.
Authors: Ahn, Y.M. / Maddumage, J.C. / Grant, E.J. / Chatzileontiadou, D.S.M. / Perera, W.W.J.G. / Baker, B.M. / Szeto, C. / Gras, S.
History
DepositionDec 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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 B alpha chain
B: Beta-2-microglobulin
C: Spike protein S2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7918
Polymers53,5593
Non-polymers2325
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-23 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.061, 82.734, 109.520
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

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen B alpha chain


Mass: 40515.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C5IYE8
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Spike protein S2'


Mass: 1164.333 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

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Non-polymers , 3 types, 326 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 14% PEG3350 and 0.1M NaFormate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.65→45.66 Å / Num. obs: 55444 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 18.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.037 / Rrim(I) all: 0.1 / Net I/σ(I): 11.9
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2692 / CC1/2: 0.793 / Rpim(I) all: 0.296 / Rrim(I) all: 0.819 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→41.37 Å / SU ML: 0.192 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.9375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2009 2825 5.1 %
Rwork0.1787 52550 -
obs0.1799 55375 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.25 Å2
Refinement stepCycle: LAST / Resolution: 1.65→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 14 321 3500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923351
X-RAY DIFFRACTIONf_angle_d1.04234565
X-RAY DIFFRACTIONf_chiral_restr0.0648473
X-RAY DIFFRACTIONf_plane_restr0.0102604
X-RAY DIFFRACTIONf_dihedral_angle_d13.76891267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.29761260.25292598X-RAY DIFFRACTION99.53
1.68-1.710.26141280.23542588X-RAY DIFFRACTION99.45
1.71-1.740.24381540.2262550X-RAY DIFFRACTION99.34
1.74-1.780.25941420.20662584X-RAY DIFFRACTION99.53
1.78-1.820.23451370.19362579X-RAY DIFFRACTION99.56
1.82-1.860.21981190.18022673X-RAY DIFFRACTION99.68
1.86-1.90.20411630.17532545X-RAY DIFFRACTION99.63
1.9-1.960.24011390.18392598X-RAY DIFFRACTION99.82
1.96-2.010.23931470.19372617X-RAY DIFFRACTION99.82
2.01-2.080.21631320.19862595X-RAY DIFFRACTION99.74
2.08-2.150.22821240.17852628X-RAY DIFFRACTION99.89
2.15-2.240.22551410.18152619X-RAY DIFFRACTION99.75
2.24-2.340.21971370.17312616X-RAY DIFFRACTION99.93
2.34-2.460.20671390.18982646X-RAY DIFFRACTION99.82
2.46-2.620.20711570.19032621X-RAY DIFFRACTION99.64
2.62-2.820.22241490.19182629X-RAY DIFFRACTION99.86
2.82-3.10.19731290.19832672X-RAY DIFFRACTION99.82
3.11-3.550.21231430.1842668X-RAY DIFFRACTION100
3.55-4.480.16871610.14562694X-RAY DIFFRACTION99.93
4.48-41.370.13591580.14512830X-RAY DIFFRACTION99.73

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