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- PDB-7lgt: HLA-B*07:02 in complex with 229E-derived coronavirus nucleocapsid... -

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Basic information

Entry
Database: PDB / ID: 7lgt
TitleHLA-B*07:02 in complex with 229E-derived coronavirus nucleocapsid peptide N75-83
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B alpha chain
  • Nucleoprotein peptide N75-83
KeywordsIMMUNE SYSTEM / HLA-B7 / 229E coronavirus / SARS-CoV-2 / T cell / recognition / cross-recognition / COVID-19
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane / 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 / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / MHC class I protein complex / defense response / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / Interferon alpha/beta signaling / 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 / iron ion transport / ER-Phagosome pathway / early endosome membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / host cell Golgi apparatus / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Nucleocapsid protein, alphacoronavirus / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid / MHC class I, alpha chain, C-terminal ...Nucleocapsid protein, alphacoronavirus / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid / 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
BROMIDE ION / : / HLA class I histocompatibility antigen, B alpha chain / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 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 21, 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 1.3Aug 11, 2021Group: Database references / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.4Oct 18, 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

Downloads & links

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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: Nucleoprotein peptide N75-83
F: Nucleoprotein peptide N75-83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,24443
Polymers90,5646
Non-polymers1,68037
Water5,909328
1
A: HLA class I histocompatibility antigen, B alpha chain
B: Beta-2-microglobulin
F: Nucleoprotein peptide N75-83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,43928
Polymers45,2823
Non-polymers1,15725
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HLA class I histocompatibility antigen, B alpha chain
D: Beta-2-microglobulin
E: Nucleoprotein peptide N75-83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,80415
Polymers45,2823
Non-polymers52212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.144, 62.854, 63.010
Angle α, β, γ (deg.)77.150, 77.000, 77.860
Int Tables number1
Space group name H-MP1

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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 Nucleoprotein peptide N75-83 / Nucleocapsid protein / NC / Protein N


Mass: 1169.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human coronavirus 229E / References: UniProt: P15130

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Non-polymers , 6 types, 365 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 3350, 0.2 M KI

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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: 1.97→44.53 Å / Num. obs: 56880 / % possible obs: 98.1 % / Redundancy: 3.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.074 / Rrim(I) all: 0.141 / Net I/σ(I): 5.5 / Num. measured all: 204851 / Scaling rejects: 69
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
1.97-2.023.70.7171431139040.5520.4380.8431.796.8
9.03-44.533.60.08621245910.9750.0540.10212.798.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTERrefinement
XDSdata reduction
Aimless0.5.12data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5wmn

5wmn


Resolution: 1.97→42.06 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 2808 4.94 %
Rwork0.1887 --
obs0.1916 56846 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.72 Å2 / Biso mean: 35.0932 Å2 / Biso min: 7.24 Å2
Refinement stepCycle: final / Resolution: 1.97→42.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6341 0 37 328 6706
Biso mean--38.48 36 -
Num. residues----767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086711
X-RAY DIFFRACTIONf_angle_d0.9559139
X-RAY DIFFRACTIONf_dihedral_angle_d20.327931
X-RAY DIFFRACTIONf_chiral_restr0.054914
X-RAY DIFFRACTIONf_plane_restr0.0061217
LS refinement shellResolution: 1.97→1.98 Å / Rfactor Rfree: 0.2514 / Rfactor Rwork: 0.2182

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