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- PDB-8elg: Crystal Structure of HLA-B*15:01 in complex with spike derived pe... -

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Basic information

Entry
Database: PDB / ID: 8elg
TitleCrystal Structure of HLA-B*15:01 in complex with spike derived peptide NQKLIANAF from OC43 virus
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • NQK-OC43 peptide
  • heavy chain HLA-B*15:01
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / TCR / T cell / HLA-B*15:01 / NQK / spike / OC43 / COVID / immune response / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / 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 / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / 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 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsMurdolo, L.D. / Gras, S.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1159272 Australia
National Health and Medical Research Council (NHMRC, Australia)Medical Research Future Fund Australia
CitationJournal: Nature / Year: 2023
Title: A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection.
Authors: Augusto, D.G. / Murdolo, L.D. / Chatzileontiadou, D.S.M. / Sabatino Jr., J.J. / Yusufali, T. / Peyser, N.D. / Butcher, X. / Kizer, K. / Guthrie, K. / Murray, V.W. / Pae, V. / ...Authors: Augusto, D.G. / Murdolo, L.D. / Chatzileontiadou, D.S.M. / Sabatino Jr., J.J. / Yusufali, T. / Peyser, N.D. / Butcher, X. / Kizer, K. / Guthrie, K. / Murray, V.W. / Pae, V. / Sarvadhavabhatla, S. / Beltran, F. / Gill, G.S. / Lynch, K.L. / Yun, C. / Maguire, C.T. / Peluso, M.J. / Hoh, R. / Henrich, T.J. / Deeks, S.G. / Davidson, M. / Lu, S. / Goldberg, S.A. / Kelly, J.D. / Martin, J.N. / Vierra-Green, C.A. / Spellman, S.R. / Langton, D.J. / Dewar-Oldis, M.J. / Smith, C. / Barnard, P.J. / Lee, S. / Marcus, G.M. / Olgin, J.E. / Pletcher, M.J. / Maiers, M. / Gras, S. / Hollenbach, J.A.
History
DepositionSep 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: heavy chain HLA-B*15:01
B: Beta-2-microglobulin
C: NQK-OC43 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0776
Polymers44,9003
Non-polymers1773
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-16 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.926, 81.550, 110.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein heavy chain HLA-B*15:01


Mass: 32132.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Beta-2-microglobulin / 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) / References: UniProt: P61769
#3: Protein/peptide NQK-OC43 peptide


Mass: 1019.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human coronavirus 229E
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2% ethylene glycol, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.956 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 1.64→46.3 Å / Num. obs: 57587 / % possible obs: 99.7 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.041 / Rrim(I) all: 0.152 / Net I/σ(I): 10.6 / Num. measured all: 764420 / Scaling rejects: 350
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
1.64-1.6711.91.3923133326350.6240.4081.4531.294.6
8.97-46.310.70.0745554250.9950.0220.07431.699.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.8data scaling
PHASERphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5TXS

5txs


Resolution: 1.65→43.2 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 2787 4.96 %
Rwork0.1827 53368 -
obs0.1846 56155 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.26 Å2 / Biso mean: 22.7642 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: final / Resolution: 1.65→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 12 510 3669
Biso mean--35.45 34.02 -
Num. residues----383
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.680.28511340.250626022736
1.68-1.710.28961380.248426582796
1.71-1.740.25681380.227126402778
1.74-1.780.29471190.212126192738
1.78-1.820.25031430.207526672810
1.82-1.860.2611420.199125982740
1.86-1.90.24591370.201626592796
1.9-1.960.22881230.197726512774
1.96-2.010.23071360.199126362772
2.01-2.080.2241370.187226312768
2.08-2.150.23981360.191726702806
2.15-2.240.24511420.186526442786
2.24-2.340.19581440.184926832827
2.34-2.460.21571430.192326502793
2.46-2.620.24951430.195526652808
2.62-2.820.2341580.193126742832
2.82-3.10.20961460.179126802826
3.11-3.550.21331350.174927212856
3.55-4.480.18361380.147327412879
4.48-43.20.18981550.161528793034

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