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- PDB-7sa2: SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented... -

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Basic information

Entry
Database: PDB / ID: 7sa2
TitleSARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Spike protein S2' peptide VVFLHVTYV
KeywordsIMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-A2 / HLA-A*02:01 / VVFLHVTYV / SARS-CoV-2 / spike
Function / homology
Function and homology information


antigen processing and presentation / 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 / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway ...antigen processing and presentation / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / MHC class II protein complex / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 receptor-mediated endocytosis / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / 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 / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / Maturation of spike protein / viral translation / Translation of Structural Proteins / host cell surface / Virion Assembly and Release / amyloid fibril formation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / Attachment and Entry / learning or memory / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / fusion of virus membrane with host plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / virion membrane / 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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Spike glycoprotein / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSzeto, C. / Gras, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01
Authors: Szeto, C. / Gras, S.
History
DepositionSep 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Spike protein S2' peptide VVFLHVTYV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3306
Polymers45,0823
Non-polymers2483
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-35 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.533, 79.242, 111.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 MHC class I antigen / HLA-A*02:01


Mass: 32125.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HLA class I histocompatibility antigen, A-2 alpha chain
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q861F7
#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
Details: Beta-2-microglobulin / 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' peptide VVFLHVTYV


Mass: 1077.294 Da / Num. of mol.: 1 / Fragment: UNP residues 1060-1068 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

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Non-polymers , 3 types, 325 molecules

#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M K formate, 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: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.85→48.1 Å / Num. obs: 46633 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 22.59 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.05 / Rrim(I) all: 0.17 / Net I/σ(I): 11.3 / Num. measured all: 532167 / Scaling rejects: 279
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
1.85-1.8911.81.5643376828580.8320.4781.6363.2100
9.06-48.19.60.07845124700.9820.0260.08322.399.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OGA

1oga


Resolution: 1.85→45.62 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.101
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2358 5.06 %RANDOM
Rwork0.174 ---
obs0.175 46566 100 %-
Displacement parametersBiso max: 136.67 Å2 / Biso mean: 26.03 Å2 / Biso min: 8.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.2885 Å20 Å20 Å2
2---0.9463 Å20 Å2
3---1.2347 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.85→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 3 322 3496
Biso mean--36.41 34.97 -
Num. residues----386
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1238SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes633HARMONIC5
X-RAY DIFFRACTIONt_it3461HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion431SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4257SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3461HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4746HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.8
X-RAY DIFFRACTIONt_other_torsion17.09
LS refinement shellResolution: 1.85→1.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2504 45 4.83 %
Rwork0.2066 887 -
all0.2084 932 -
obs--100 %

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