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- PDB-7lg0: Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope... -

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Basic information

Entry
Database: PDB / ID: 7lg0
TitleHuman leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope SPRWYFYYL
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-7 alpha chain
  • Nucleoprotein
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / SARS-CoV2 / CD8+ / epitope / HLA / human major histocompatibility complex / SPRWYFYYL / HLA-B7 / HLA-B*07:02 / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / regulation of interleukin-12 production / regulation of dendritic cell differentiation / Maturation of nucleoprotein / regulation of T cell anergy ...SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / regulation of interleukin-12 production / regulation of dendritic cell differentiation / Maturation of nucleoprotein / regulation of T cell anergy / regulation of interleukin-6 production / SARS-CoV-1 modulates host translation machinery / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / 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 / SARS-CoV-1 activates/modulates innate immune responses / 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 / viral capsid / 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 / molecular adaptor activity / learning or memory / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion
Similarity search - Function
Nucleocapsid protein, betacoronavirus / 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, betacoronavirus / 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
HLA class I histocompatibility antigen, B alpha chain / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPatskovska, L. / Patskovsky, Y. / Krogsgaard, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA243486-01A1 United States
CitationJournal: To Be Published
Title: Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope SPRWYFYYL
Authors: Patskovska, L. / Patskovsky, Y. / Krogsgaard, M.
History
DepositionJan 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-7 alpha chain
B: Beta-2-microglobulin
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4194
Polymers45,1373
Non-polymers2821
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-17 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.723, 155.172, 88.165
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

21C-101-

HOH

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Components

#1: Protein HLA class I histocompatibility antigen, B-7 alpha chain / MHC class I antigen B*7


Mass: 31962.016 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01889
#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
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 1295.464 Da / Num. of mol.: 1 / Fragment: UNP residues 105-113 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus
References: UniProt: P59595
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES-NaOH, pH 7.5, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2020 / Details: SI 111 CRYSTAL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.296→41.95 Å / Num. obs: 22281 / % possible obs: 99.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.1 / Χ2: 1 / Net I/σ(I): 8.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1096 / CC1/2: 0.84 / CC star: 0.95 / Χ2: 0.99 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6AT5

6at5


Resolution: 2.3→41.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.331 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 657 3 %RANDOM
Rwork0.2001 ---
obs0.2021 21542 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.6 Å / VDW probe radii: 0.8 Å / Solvent model: MASK
Displacement parametersBiso max: 133.9 Å2 / Biso mean: 50.251 Å2 / Biso min: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å2-0 Å20 Å2
2---4.54 Å2-0 Å2
3---0.86 Å2
Refinement stepCycle: final / Resolution: 2.3→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 19 158 3326
Biso mean--69.41 52.51 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133320
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172844
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.6644519
X-RAY DIFFRACTIONr_angle_other_deg1.1961.5936604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0795395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19821.69213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47615516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9941529
X-RAY DIFFRACTIONr_chiral_restr0.0550.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02769
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 51 -
Rwork0.305 1574 -
all-1625 -
obs--99.94 %

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