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- PDB-7n1d: SARS-CoV-2 YLQ peptide-specific TCR pYLQ7 -

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Basic information

Entry
Database: PDB / ID: 7n1d
TitleSARS-CoV-2 YLQ peptide-specific TCR pYLQ7
Components
  • pYLQ7 T cell receptor alpha chain
  • pYLQ7 T cell receptor beta chain
KeywordsIMMUNE SYSTEM / TCR / SARS-CoV-2 / SPIKE / YLQ
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1.2Feb 2, 2022Group: Database references / Category: citation / citation_author
Revision 1.3Oct 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
Item: _citation.journal_id_ISSN
Revision 1.4Nov 20, 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: pYLQ7 T cell receptor alpha chain
B: pYLQ7 T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)49,7662
Polymers49,7662
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-27 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.777, 109.777, 99.641
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein pYLQ7 T cell receptor alpha chain


Mass: 22282.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: T cell receptor alpha chain / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein pYLQ7 T cell receptor beta chain


Mass: 27483.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: T cell receptor beta chain / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.2M Potassium sodium tartrate tetrahydrate, 0.1M Tris-base/ Hydrochloric acid (pH 8.0)

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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: 2.35→38.812 Å / Num. obs: 24641 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.994 / Net I/σ(I): 12.84
Reflection shellResolution: 2.35→2.434 Å / Num. unique obs: 2476 / CC1/2: 0.832

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XQP, 4UDT

6xqp

4udt


Resolution: 2.35→38.812 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2722 1119 4.54 %
Rwork0.2042 23522 -
obs0.2072 24641 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.32 Å2 / Biso mean: 47.5435 Å2 / Biso min: 21.17 Å2
Refinement stepCycle: final / Resolution: 2.35→38.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 0 142 3615
Biso mean---47.59 -
Num. residues----439
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3502-2.45710.35251340.26022907
2.4571-2.58660.31571470.24282937
2.5866-2.74860.28251370.24412933
2.7486-2.96080.29451650.22982921
2.9608-3.25860.32791430.22332911
3.2586-3.72980.29041420.19942929
3.7298-4.69790.24011260.17942960
4.6979-38.8120.22461250.18893024

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