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- PDB-7lgd: HLA-B*07:02 in complex with SARS-CoV-2 nucleocapsid peptide N105-113 -

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Basic information

Entry
Database: PDB / ID: 7lgd
TitleHLA-B*07:02 in complex with SARS-CoV-2 nucleocapsid peptide N105-113
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B alpha chain
  • SARS-CoV-2 nucleocapsid peptide N105-113
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / HLA / T cell / cross-reactivity / COVID-19 / antigen presentation
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / regulation of interleukin-12 production / negative regulation of interferon-beta production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Maturation of nucleoprotein / poly(U) RNA binding ...: / response to host immune response / viral RNA genome packaging / regulation of interleukin-12 production / negative regulation of interferon-beta production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Maturation of nucleoprotein / poly(U) RNA binding / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / CD28 dependent PI3K/Akt signaling / detection of bacterium / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / secretory granule membrane / 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 / 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 / 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 / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / DDX58/IFIH1-mediated induction of interferon-alpha/beta / 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 / protein-folding chaperone binding / 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 / adaptive immune response / 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
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
HLA class I histocompatibility antigen, B alpha chain / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.88 Å
AuthorsGras, S. / Szeto, C. / Chatzileontiadou, D.S.M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
Australian Research Council (ARC) Australia
CitationJournal: Immunity / Year: 2021
Title: CD8 + T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses.
Authors: Lineburg, K.E. / Grant, E.J. / Swaminathan, S. / Chatzileontiadou, D.S.M. / Szeto, C. / Sloane, H. / Panikkar, A. / Raju, J. / Crooks, P. / Rehan, S. / Nguyen, A.T. / Lekieffre, L. / Neller, ...Authors: Lineburg, K.E. / Grant, E.J. / Swaminathan, S. / Chatzileontiadou, D.S.M. / Szeto, C. / Sloane, H. / Panikkar, A. / Raju, J. / Crooks, P. / Rehan, S. / Nguyen, A.T. / Lekieffre, L. / Neller, M.A. / Tong, Z.W.M. / Jayasinghe, D. / Chew, K.Y. / Lobos, C.A. / Halim, H. / Burrows, J.M. / Riboldi-Tunnicliffe, A. / Chen, W. / D'Orsogna, L. / Khanna, R. / Short, K.R. / Smith, C. / Gras, S.
History
DepositionJan 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 26, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 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

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, B alpha chain
D: Beta-2-microglobulin
E: SARS-CoV-2 nucleocapsid peptide N105-113
F: SARS-CoV-2 nucleocapsid peptide N105-113
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,40116
Polymers90,8166
Non-polymers58510
Water73941
1
A: HLA class I histocompatibility antigen, B alpha chain
B: Beta-2-microglobulin
F: SARS-CoV-2 nucleocapsid peptide N105-113
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5146
Polymers45,4083
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-37 kcal/mol
Surface area19780 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, B alpha chain
D: Beta-2-microglobulin
E: SARS-CoV-2 nucleocapsid peptide N105-113
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,88610
Polymers45,4083
Non-polymers4787
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-83 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.454, 107.176, 174.190
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, 4 molecules ACBD

#1: Protein HLA class I histocompatibility antigen, B alpha chain / Human leukocyte antigen B / HLA-B


Mass: 32233.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P01889
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide SARS-CoV-2 nucleocapsid peptide N105-113


Mass: 1295.464 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9

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Non-polymers , 4 types, 51 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2M Ammonium Sulfate, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.88→46.65 Å / Num. obs: 28141 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.898 / Rmerge(I) obs: 0.195 / Net I/σ(I): 8 / Num. measured all: 191654 / Scaling rejects: 165
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.88-3.046.61.2622645340270.5781.6100
9.11-46.656.10.066618010050.99418.399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTERrefinement
XDSdata reduction
Aimless0.5.1data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5wmn

5wmn


Resolution: 2.88→43.55 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.52 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2692 1455 5.18 %RANDOM
Rwork0.2058 ---
obs0.2091 28078 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.61 Å2 / Biso mean: 55.6076 Å2 / Biso min: 18.37 Å2
Refinement stepCycle: final / Resolution: 2.88→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6386 0 26 41 6453
Biso mean--80.76 37.17 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096611
X-RAY DIFFRACTIONf_angle_d1.0388983
X-RAY DIFFRACTIONf_dihedral_angle_d14.917888
X-RAY DIFFRACTIONf_chiral_restr0.057891
X-RAY DIFFRACTIONf_plane_restr0.0061190
LS refinement shellResolution: 2.88→3.04 Å / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.269

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