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

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Basic information

Entry
Database: PDB / ID: 6vth
Titlep53-specific T cell receptor
Components
  • T-cell Receptor 12-6, Alfa chain
  • TCR 12-6, beta 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: 2.36 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell Receptor 12-6, Alfa chain
B: TCR 12-6, beta chain
D: T-cell Receptor 12-6, Alfa chain
E: TCR 12-6, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4385
Polymers101,3424
Non-polymers961
Water6,251347
1
A: T-cell Receptor 12-6, Alfa chain
B: TCR 12-6, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7673
Polymers50,6712
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-27 kcal/mol
Surface area20000 Å2
MethodPISA
2
D: T-cell Receptor 12-6, Alfa chain
E: TCR 12-6, beta chain


Theoretical massNumber of molelcules
Total (without water)50,6712
Polymers50,6712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-37 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.615, 84.955, 88.749
Angle α, β, γ (deg.)90.000, 93.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein T-cell Receptor 12-6, Alfa chain


Mass: 22881.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein TCR 12-6, beta chain


Mass: 27789.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6 / Details: 18% (w/v) PEG 2000, 0.2 M AmSO4, 0.1 M MES

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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: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→39.3 Å / Num. obs: 36665 / % possible obs: 91.1 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.9
Reflection shellResolution: 2.36→2.44 Å / Rmerge(I) obs: 0.263 / Num. unique obs: 3669

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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: 3sjv, 2ak4

3sjv

2ak4


Resolution: 2.36→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 14.97 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.294 / Details: TLS
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 1783 4.9 %RANDOM
Rwork0.2115 ---
obs0.214 34799 90.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.19 Å2 / Biso mean: 39.584 Å2 / Biso min: 18.21 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å20 Å20.26 Å2
2--2.8 Å20 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 2.36→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6694 0 5 347 7046
Biso mean--35.76 44.91 -
Num. residues----867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126874
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.6379370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6265857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04423.164354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.502151025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8771533
X-RAY DIFFRACTIONr_chiral_restr0.090.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025380
LS refinement shellResolution: 2.36→2.419 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.279 91 -
Rwork0.225 2539 -
obs--89.91 %
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)
10.3849-0.16930.27980.1053-0.07330.59990.00070.1008-0.03310.0007-0.01190.0074-0.00170.04940.01130.0067-0.0102-0.00740.0937-0.01490.018514.295716.344798.0453
20.5352-0.13520.20980.2057-0.08740.25250.0494-0.0331-0.06030.0336-0.00710.0401-0.0101-0.0112-0.04230.0298-0.0164-0.00220.038-0.00380.01771.33299.8369111.534
30.37390.11010.14570.11980.25710.5821-0.0035-0.0995-0.02150.007-0.03420.01210.0167-0.05270.03770.00850.00880.00240.07640.02580.015710.930915.6397162.3716
40.69240.15470.37680.08380.20540.53090.02420.0271-0.0909-0.01070.0152-0.0183-0.00980.03-0.03940.02440.014-0.00210.0497-0.0070.01323.96189.2049148.9952
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 200
2X-RAY DIFFRACTION2B3 - 244
3X-RAY DIFFRACTION3D3 - 200
4X-RAY DIFFRACTION4E3 - 245

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