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- PDB-7kgt: Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N226-234 -

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Basic information

Entry
Database: PDB / ID: 7kgt
TitleCrystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N226-234
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Nucleoprotein
KeywordsIMMUNE SYSTEM / HLA-A*0201 / T cell / SARS-CoV-2 / COVID-19 / viral peptide / TCR
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / antigen processing and presentation of peptide antigen via MHC class I ...: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / antigen processing and presentation of peptide antigen via MHC class I / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / VEGFR2 mediated vascular permeability / 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 / molecular condensate scaffold activity / 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 / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / DDX58/IFIH1-mediated induction of interferon-alpha/beta / 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 / RNA stem-loop binding / specific granule lumen / Interleukin-1 signaling / 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 / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / viral capsid / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / PIP3 activates AKT signaling / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / early endosome membrane / protein homotetramerization / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / amyloid fibril formation / Induction of Cell-Cell Fusion / intracellular iron ion homeostasis / Attachment and Entry / learning or memory / host cell perinuclear region of cytoplasm / immune response / endoplasmic reticulum lumen / ribonucleoprotein complex / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / MHC class I, alpha chain, C-terminal ...Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / 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 / : / Nucleoprotein / 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 / molecular replacement / Resolution: 1.9 Å
AuthorsSzeto, C. / Chatzileontiadou, D.S.M. / Riboldi-Tunnicliffe, A. / Gras, S.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1110429 Australia
National Health and Medical Research Council (NHMRC, Australia)1159272 Australia
CitationJournal: Iscience / Year: 2021
Title: The presentation of SARS-CoV-2 peptides by the common HLA-A*02:01 molecule.
Authors: Szeto, C. / Chatzileontiadou, D.S.M. / Nguyen, A.T. / Sloane, H. / Lobos, C.A. / Jayasinghe, D. / Halim, H. / Smith, C. / Riboldi-Tunnicliffe, A. / Grant, E.J. / Gras, S.
History
DepositionOct 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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: MHC class I antigen
B: Beta-2-microglobulin
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3297
Polymers45,0223
Non-polymers3074
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-30 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.287, 79.684, 111.117
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


Mass: 32153.523 Da / Num. of mol.: 1 / Mutation: A245V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q861F7
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 1120.323 Da / Num. of mol.: 1 / Fragment: residues 226-234 / Source method: obtained synthetically / Details: synthesized
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9

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Non-polymers , 4 types, 417 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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.96 Å3/Da / Density % sol: 58.5 % / Mosaicity: 0.15 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG3350 w/v, 0.2M KFormate, 1mM CdCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 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: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.9→48.08 Å / Num. obs: 42802 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.136 / Net I/σ(I): 10.1 / Num. measured all: 289860 / Scaling rejects: 624
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.9-1.946.61.3171777127040.7582.399
9.11-48.085.50.05625174600.99421.199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimless0.5.1data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GSO

3gso


Resolution: 1.9→45.57 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 2146 5.02 %
Rwork0.1692 40589 -
obs0.1709 42735 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.97 Å2 / Biso mean: 25.5147 Å2 / Biso min: 8.35 Å2
Refinement stepCycle: final / Resolution: 1.9→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 7 413 3544
Biso mean--39.45 34.42 -
Num. residues----380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.940.30451460.24762652279899
1.94-1.990.28961390.213426712810100
1.99-2.050.22271290.19962659278899
2.05-2.110.261530.19262636278999
2.11-2.170.20761410.1842674281599
2.18-2.250.22361440.18232641278599
2.25-2.340.22431480.17622678282699
2.34-2.450.22881680.177126472815100
2.45-2.580.2741220.180627452867100
2.58-2.740.22861380.17927042842100
2.74-2.950.20851300.183127232853100
2.95-3.250.19181490.172927152864100
3.25-3.720.20081520.160327532905100
3.72-4.680.13351340.129327872921100
4.68-45.570.18371530.15429043057100

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