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- PDB-8gop: SARS-CoV-2 specific private TCR RLQ7 -

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Basic information

Entry
Database: PDB / ID: 8gop
TitleSARS-CoV-2 specific private TCR RLQ7
Components
  • SARS-CoV-2 specific private TCR RLQ7 alpha
  • SARS-CoV-2 specific private TCR RLQ7 beta
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / Private TCR / TCR-p-HLA
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWu, D. / Mariuzza, R.A.
Funding support United States, China, 3items
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
National Natural Science Foundation of China (NSFC)32100985 China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural insights into protection against a SARS-CoV-2 spike variant by T cell receptor (TCR) diversity.
Authors: Wu, D. / Efimov, G.A. / Bogolyubova, A.V. / Pierce, B.G. / Mariuzza, R.A.
History
DepositionAug 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 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
B: SARS-CoV-2 specific private TCR RLQ7 beta
A: SARS-CoV-2 specific private TCR RLQ7 alpha


Theoretical massNumber of molelcules
Total (without water)51,0882
Polymers51,0882
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-27 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.178, 68.054, 63.878
Angle α, β, γ (deg.)90.000, 90.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SARS-CoV-2 specific private TCR RLQ7 beta


Mass: 27912.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein SARS-CoV-2 specific private TCR RLQ7 alpha


Mass: 23175.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02 M Sodium phosphate monobasic, 0.1M Bis-Tris propane pH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→34.8 Å / Num. obs: 10990 / % possible obs: 94.48 % / Redundancy: 9.39 % / CC1/2: 0.842 / Net I/σ(I): 9.39
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 1107 / CC1/2: 0.647

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GOM

8gom


Resolution: 2.8→34.8 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2862 474 4.32 %
Rwork0.2311 10510 -
obs0.2333 10984 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.33 Å2 / Biso mean: 35.4613 Å2 / Biso min: 20.55 Å2
Refinement stepCycle: final / Resolution: 2.8→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 0 0 117 3600
Biso mean---29.54 -
Num. residues----443
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-3.20490.37531710.2863347499
3.2049-4.03690.32331320.2362350998
4.0369-34.80.23381710.2051352798

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