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- PDB-8rbv: SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (VLNDILARL... -

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Basic information

Entry
Database: PDB / ID: 8rbv
TitleSARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (VLNDILARL) presented by HLA-A*02:01
Components
  • Beta-2-microglobulin
  • HLA class I antigen
  • SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant
KeywordsIMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-A2 / HLA-A*02:01 / 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 / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane ...antigen processing and presentation of peptide antigen via MHC class I / : / : / negative regulation of receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / 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 / 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 / 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 / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / positive regulation of protein binding / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / 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 / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / iron ion transport / 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 / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / 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
ACETATE ION / : / DI(HYDROXYETHYL)ETHER / Beta-2-microglobulin / HLA class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 5, 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 6, 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 antigen
B: Beta-2-microglobulin
C: SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,45510
Polymers53,8813
Non-polymers5737
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-19 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.821, 78.177, 110.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I antigen


Mass: 40974.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q53Z42
#2: Protein 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 SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant


Mass: 1027.239 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2

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Non-polymers , 5 types, 225 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 13% P3350; 0.1M NaFlu; 2% EG; 1 mM CdCl2

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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: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.8→47.51 Å / Num. obs: 49032 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 29.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.036 / Rrim(I) all: 0.099 / Net I/σ(I): 12 / Num. measured all: 359908 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.847.51.2342150128810.6320.4841.3261.7100
9-47.516.20.04228534630.9980.0170.0453499.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.23 Å47.51 Å
Translation6.23 Å47.51 Å

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5127: ???)refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OGA

1oga


Resolution: 1.8→43.67 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2511 5.13 %RANDOM
Rwork0.1797 ---
obs0.1814 48961 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 25 218 3403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063333
X-RAY DIFFRACTIONf_angle_d0.8234528
X-RAY DIFFRACTIONf_dihedral_angle_d14.2621234
X-RAY DIFFRACTIONf_chiral_restr0.054465
X-RAY DIFFRACTIONf_plane_restr0.007594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.31171400.25912553X-RAY DIFFRACTION100
1.83-1.870.29261570.24752517X-RAY DIFFRACTION100
1.87-1.910.23761300.23932555X-RAY DIFFRACTION100
1.91-1.960.30661470.22722540X-RAY DIFFRACTION100
1.96-2.010.25991250.21492563X-RAY DIFFRACTION100
2.01-2.060.24181540.20092548X-RAY DIFFRACTION100
2.06-2.120.20771230.18762535X-RAY DIFFRACTION100
2.12-2.190.21181320.1852564X-RAY DIFFRACTION100
2.19-2.270.20441200.18922580X-RAY DIFFRACTION100
2.27-2.360.21591180.18312592X-RAY DIFFRACTION100
2.36-2.470.20381410.1832573X-RAY DIFFRACTION100
2.47-2.60.21461360.18762575X-RAY DIFFRACTION100
2.6-2.760.2171480.18732555X-RAY DIFFRACTION100
2.76-2.970.22251450.19622586X-RAY DIFFRACTION100
2.97-3.270.22051440.19982591X-RAY DIFFRACTION100
3.27-3.740.21191470.17972612X-RAY DIFFRACTION100
3.74-4.720.18151460.13832644X-RAY DIFFRACTION100
4.72-43.670.1861580.15742767X-RAY DIFFRACTION100

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