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- PDB-6vtc: p53-specific T cell receptor -

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Basic information

Entry
Database: PDB / ID: 6vtc
Titlep53-specific T cell receptor
Components
  • T-cell Receptor 1a2
  • p53-specific T cell receptor, B-chain
KeywordsIMMUNE SYSTEM / TCR complex / MHC / HLA / adoptive cell therapy
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsWu, D. / Gallagher, D.T. / Gowthaman, R. / Pierce, B.G. / Mariuzza, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126299 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen.
Authors: Wu, D. / Gallagher, D.T. / Gowthaman, R. / Pierce, B.G. / Mariuzza, R.A.
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 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
A: T-cell Receptor 1a2
B: p53-specific T cell receptor, B-chain


Theoretical massNumber of molelcules
Total (without water)51,1702
Polymers51,1702
Non-polymers00
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-28 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.123, 106.369, 112.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein T-cell Receptor 1a2


Mass: 23348.869 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 p53-specific T cell receptor, B-chain


Mass: 27821.088 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.: 391 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6 / Details: 20% (w/v) PEG 4000, 0.2 M LiSO4, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→31.3 Å / Num. obs: 44465 / % possible obs: 99.7 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 30.6
Reflection shellResolution: 1.83→1.9 Å / Rmerge(I) obs: 0.328 / Num. unique obs: 4396

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3utp, 3vxt

3utp

3vxt


Resolution: 1.83→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.302 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.13
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 2172 4.9 %RANDOM
Rwork0.1903 ---
obs0.1923 42266 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.54 Å2 / Biso mean: 42.458 Å2 / Biso min: 22.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å2-0 Å20 Å2
2---0.42 Å20 Å2
3----2.61 Å2
Refinement stepCycle: final / Resolution: 1.83→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 0 0 391 3824
Biso mean---52.65 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0123523
X-RAY DIFFRACTIONr_angle_refined_deg2.1621.6394799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6325437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62923.152184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01615546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3711518
X-RAY DIFFRACTIONr_chiral_restr0.1720.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022753
LS refinement shellResolution: 1.83→1.877 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 153 -
Rwork0.261 3079 -
all-3232 -
obs--99.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.12160.16580.08280.6569-0.13570.20420.04710.0406-0.01640.0138-0.033-0.0250.05480.0975-0.01410.02770.0075-0.00460.1063-0.01880.08555.370716.61915.7285
20.0532-0.13620.15720.4401-0.26460.6982-0.01560.01960.00040.0446-0.0430.0024-0.04320.06810.05860.0066-0.0178-0.00130.10450.01160.09879.311324.796322.9948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 204
2X-RAY DIFFRACTION2B1 - 243

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