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- PDB-8rhq: Crystal structure of HLA-A*11:01 in complex with SVLNDIFSRL, an 1... -

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Basic information

Entry
Database: PDB / ID: 8rhq
TitleCrystal structure of HLA-A*11:01 in complex with SVLNDIFSRL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen
  • Spike protein S2'
KeywordsIMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-A11 / HLA-A*11:01 / SARS-CoV-2 / Spike
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / 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 / symbiont-mediated disruption of host tissue / protein homotetramerization / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / amyloid fibril formation / Induction of Cell-Cell Fusion / structural constituent of virion / intracellular iron ion homeostasis / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / learning or memory / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / immune response / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome
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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Spike glycoprotein / Beta-2-microglobulin / HLA class I histocompatibility antigen A alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 16, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Beta-2-microglobulin
C: HLA class I histocompatibility antigen
D: Beta-2-microglobulin
E: HLA class I histocompatibility antigen
F: Beta-2-microglobulin
G: Spike protein S2'
H: Spike protein S2'
I: Spike protein S2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,44934
Polymers162,0889
Non-polymers1,36125
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20730 Å2
ΔGint-61 kcal/mol
Surface area53290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.492, 85.492, 312.028
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein HLA class I histocompatibility antigen / HLA class I histocompatibility antigen A alpha chain / MHC class I antigen / MHC class I protein / ...HLA class I histocompatibility antigen A alpha chain / MHC class I antigen / MHC class I protein / MHC class I protein (HLA-A)


Mass: 40985.727 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLA, HLA-A11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5S3G3
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 3 / 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, 3 molecules GHI

#3: Protein/peptide Spike protein S2'


Mass: 1164.333 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

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Non-polymers , 6 types, 571 molecules

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


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M Sodium acetate tihydrate pH 7.0

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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: Feb 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2→47.72 Å / Num. obs: 90742 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 25.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.034 / Rrim(I) all: 0.151 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 19 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 4424 / CC1/2: 0.947 / Rpim(I) all: 0.14 / Rrim(I) all: 0.612 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.75 Å / SU ML: 0.2321 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0115
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2443 4539 5.01 %
Rwork0.1981 86086 -
obs0.2004 90625 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.27 Å2
Refinement stepCycle: LAST / Resolution: 2→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9433 0 82 546 10061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00449883
X-RAY DIFFRACTIONf_angle_d0.65113383
X-RAY DIFFRACTIONf_chiral_restr0.04591362
X-RAY DIFFRACTIONf_plane_restr0.00671767
X-RAY DIFFRACTIONf_dihedral_angle_d12.72743700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.2621480.23152801X-RAY DIFFRACTION100
2.02-2.050.31071370.22782813X-RAY DIFFRACTION99.97
2.05-2.070.28871600.22042851X-RAY DIFFRACTION100
2.07-2.10.28341400.21422818X-RAY DIFFRACTION100
2.1-2.130.26171180.22012855X-RAY DIFFRACTION100
2.13-2.150.2991230.2122877X-RAY DIFFRACTION100
2.15-2.190.2731500.2122842X-RAY DIFFRACTION100
2.19-2.220.24411310.20842827X-RAY DIFFRACTION100
2.22-2.250.25991810.20212827X-RAY DIFFRACTION100
2.25-2.290.26871380.20542810X-RAY DIFFRACTION100
2.29-2.330.27471410.20982879X-RAY DIFFRACTION100
2.33-2.370.27611660.21342849X-RAY DIFFRACTION100
2.37-2.420.27371650.20632788X-RAY DIFFRACTION100
2.42-2.470.28311640.21372845X-RAY DIFFRACTION100
2.47-2.520.26231560.2172854X-RAY DIFFRACTION100
2.52-2.580.27151310.20592848X-RAY DIFFRACTION99.97
2.58-2.640.2581850.21942816X-RAY DIFFRACTION100
2.64-2.710.26331530.21542835X-RAY DIFFRACTION100
2.71-2.790.2811560.21672866X-RAY DIFFRACTION100
2.79-2.880.26271680.2142831X-RAY DIFFRACTION100
2.88-2.990.26311510.21142885X-RAY DIFFRACTION99.97
2.99-3.110.25451690.22192854X-RAY DIFFRACTION100
3.11-3.250.24781630.20882856X-RAY DIFFRACTION100
3.25-3.420.22851340.2032947X-RAY DIFFRACTION100
3.42-3.630.24661480.19562868X-RAY DIFFRACTION100
3.63-3.910.20211480.1762932X-RAY DIFFRACTION100
3.91-4.310.21321270.16062936X-RAY DIFFRACTION100
4.31-4.930.20581530.1592946X-RAY DIFFRACTION99.94
4.93-6.210.20961390.18863009X-RAY DIFFRACTION99.97
6.21-42.750.20741960.18643121X-RAY DIFFRACTION99.79

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