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- PDB-7n1b: SARS-CoV-2 RLQ peptide binds to HLA-A2 -

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Basic information

Entry
Database: PDB / ID: 7n1b
TitleSARS-CoV-2 RLQ peptide binds to HLA-A2
Components
  • Beta-2-microglobulin
  • MHC class I antigen, A-2 alpha chain
  • Spike protein S2
KeywordsIMMUNE SYSTEM / pMHC / SARS-CoV-2 / SPIKE / RLQ
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport ...antigen processing and presentation of peptide antigen via MHC class I / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of immune response / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / ER-Phagosome pathway / symbiont-mediated disruption of host tissue / early endosome membrane / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / amyloid fibril formation / protein homotetramerization / positive regulation of viral entry into host cell / Initial triggering of complement / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / intracellular iron ion homeostasis / learning or memory / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / immune response / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / receptor ligand activity / Amyloid fiber formation / external side of plasma membrane / fusion of virus membrane with host plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
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. ...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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Spike glycoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsWu, D. / Mariuzza, R.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI129893 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126299 United States
Citation
Journal: Nat Commun / Year: 2022
Title: Structural assessment of HLA-A2-restricted SARS-CoV-2 spike epitopes recognized by public and private T-cell receptors.
Authors: Wu, D. / Kolesnikov, A. / Yin, R. / Guest, J.D. / Gowthaman, R. / Shmelev, A. / Serdyuk, Y. / Dianov, D.V. / Efimov, G.A. / Pierce, B.G. / Mariuzza, R.A.
#1: Journal: Biorxiv / Year: 2021
Title: Structural basis for recognition of two HLA-A2-restricted SARS-CoV-2 spike epitopes by public and private T cell receptors
Authors: Wu, D. / Kolesnikov, A. / Yin, R. / Guest, J.D. / Gowthaman, R. / Shmelev, A. / Serdyuk, Y. / Efimov, G.A. / Pierce, B.G. / Mariuzza, R.A.
History
DepositionMay 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Sep 22, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / pdbx_struct_assembly_prop ...atom_site / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_ls_restr_ncs / refine_ls_shell / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_assembly_prop.value / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.pdbx_overall_phase_error / _refine_ls_restr_ncs.pdbx_rms / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet.number_strands
Description: Real space R-factor / Provider: author / Type: Coordinate replacement
Revision 2.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Revision 2.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id ..._citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Spike protein S2
D: MHC class I antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Spike protein S2


Theoretical massNumber of molelcules
Total (without water)89,6846
Polymers89,6846
Non-polymers00
Water00
1
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Spike protein S2


Theoretical massNumber of molelcules
Total (without water)44,8423
Polymers44,8423
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-18 kcal/mol
Surface area18910 Å2
MethodPISA
2
D: MHC class I antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Spike protein S2


Theoretical massNumber of molelcules
Total (without water)44,8423
Polymers44,8423
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-19 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.204, 49.259, 117.094
Angle α, β, γ (deg.)91.890, 92.390, 118.590
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resid 1 through 107 or (resid 108...
21(chain D and (resid 1 through 254 or (resid 255...
12chain B
22chain E
13chain C
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYTRPTRP(chain A and (resid 1 through 107 or (resid 108...AA1 - 1071 - 107
121ARGARGARGARG(chain A and (resid 1 through 107 or (resid 108...AA108108
131GLYGLYTRPTRP(chain A and (resid 1 through 107 or (resid 108...AA1 - 2741 - 274
141GLYGLYTRPTRP(chain A and (resid 1 through 107 or (resid 108...AA1 - 2741 - 274
151GLYGLYTRPTRP(chain A and (resid 1 through 107 or (resid 108...AA1 - 2741 - 274
161GLYGLYTRPTRP(chain A and (resid 1 through 107 or (resid 108...AA1 - 2741 - 274
211GLYGLYGLUGLU(chain D and (resid 1 through 254 or (resid 255...DD1 - 2541 - 254
221GLNGLNGLNGLN(chain D and (resid 1 through 254 or (resid 255...DD255255
231GLYGLYLEULEU(chain D and (resid 1 through 254 or (resid 255...DD1 - 2721 - 272
112METMETMETMETchain BBB0 - 991 - 100
212METMETMETMETchain EEE0 - 991 - 100
113ARGARGVALVALchain CCC1 - 91 - 9
213ARGARGVALVALchain FFF1 - 91 - 9

NCS ensembles :
ID
1
2
3

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Components

#1: Protein MHC class I antigen, A-2 alpha chain


Mass: 31854.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B8RNS7
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide Spike protein S2


Mass: 1108.268 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M MES (pH 6.5), 20% (w/v) PEG 8000 by micro-seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.81→43.2 Å / Num. obs: 37697 / % possible obs: 96.1 % / Redundancy: 1.7 % / CC1/2: 0.911 / Net I/σ(I): 9.4
Reflection shellResolution: 2.81→2.91 Å / Num. unique obs: 3276 / CC1/2: 0.638

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VR5

6vr5


Resolution: 2.81→43.174 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2691 1074 4.96 %
Rwork0.2111 20571 -
obs0.2138 21645 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.75 Å2 / Biso mean: 31.2391 Å2 / Biso min: 4.33 Å2
Refinement stepCycle: final / Resolution: 2.81→43.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 0 0 6261
Num. residues----764
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1668X-RAY DIFFRACTION5.071TORSIONAL
12D1668X-RAY DIFFRACTION5.071TORSIONAL
21B606X-RAY DIFFRACTION5.071TORSIONAL
22E606X-RAY DIFFRACTION5.071TORSIONAL
31C52X-RAY DIFFRACTION5.071TORSIONAL
32F52X-RAY DIFFRACTION5.071TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.81-2.93740.34581530.2554241189
2.9374-3.09220.32891510.242253295
3.0922-3.28590.3161440.2351255596
3.2859-3.53950.29481200.2259258897
3.5395-3.89540.27241270.1945260297
3.8954-4.45860.21751190.182264998
4.4586-5.61540.223720.1847265198
5.6154-43.1740.22741880.2241258398

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