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- PDB-6vqo: T cell receptor-p53-HLA-A2 complex -

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Basic information

Entry
Database: PDB / ID: 6vqo
TitleT cell receptor-p53-HLA-A2 complex
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • T-cell receptor 1a2, alfa chain
  • TCR receptor 1a2, beta chain
  • peptide from p53 tumor suppressor
KeywordsIMMUNE SYSTEM / TCR complex / MHC / HLA / adoptive cell therapy
Function / homology
Function and homology information


Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / T cell lineage commitment / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / B cell lineage commitment / thymocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / T cell proliferation involved in immune response / negative regulation of reactive oxygen species metabolic process / positive regulation of execution phase of apoptosis / Transcriptional Regulation by VENTX / replicative senescence / cellular response to UV-C / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to actinomycin D / neuroblast proliferation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / type II interferon-mediated signaling pathway / hematopoietic stem cell differentiation / Pyroptosis / chromosome organization / viral process / embryonic organ development / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / mitophagy / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / positive regulation of intrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / negative regulation of proteolysis / Regulation of TP53 Activity through Acetylation / mitotic G1 DNA damage checkpoint signaling / gastrulation / 14-3-3 protein binding / response to salt stress
Similarity search - Function
Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family ...Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Major histocompatibility complex, class I, A / MHC class I antigen / Cellular tumor antigen p53 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsWu, D. / Gallagher, D.T. / 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 5, 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
D: T-cell receptor 1a2, alfa chain
E: TCR receptor 1a2, beta chain
F: MHC class I antigen
G: Beta-2-microglobulin
H: T-cell receptor 1a2, alfa chain
J: TCR receptor 1a2, beta chain
P: peptide from p53 tumor suppressor
Q: peptide from p53 tumor suppressor


Theoretical massNumber of molelcules
Total (without water)196,15210
Polymers196,15210
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
D: T-cell receptor 1a2, alfa chain
E: TCR receptor 1a2, beta chain
P: peptide from p53 tumor suppressor


Theoretical massNumber of molelcules
Total (without water)98,0765
Polymers98,0765
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: MHC class I antigen
G: Beta-2-microglobulin
H: T-cell receptor 1a2, alfa chain
J: TCR receptor 1a2, beta chain
Q: peptide from p53 tumor suppressor


Theoretical massNumber of molelcules
Total (without water)98,0765
Polymers98,0765
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.130, 118.130, 153.129
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein MHC class I antigen


Mass: 33912.469 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 (E. coli) / References: UniProt: F6IQS2, UniProt: A0A140T913*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein T-cell receptor 1a2, alfa chain


Mass: 23348.869 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)
#4: Protein TCR receptor 1a2, beta chain


Mass: 27821.088 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)
#5: Protein/peptide peptide from p53 tumor suppressor


Mass: 1114.320 Da / Num. of mol.: 2 / Mutation: R175H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04637*PLUS
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: 3.14 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8 / Details: 12% (w/v) PEG 8000, 0.1 M magnesium acetate

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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 6M / Detector: PIXEL / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48.8 Å / Num. obs: 47556 / % possible obs: 97.1 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.477 / Num. unique obs: 3813

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3utp, 3vxt, 5d2l

3utp

3vxt

5d2l


Resolution: 3→48.52 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.883 / SU B: 30.419 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.074 / Details: TLS
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 2260 4.9 %RANDOM
Rwork0.1618 ---
obs0.1642 43889 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 150.16 Å2 / Biso mean: 53.444 Å2 / Biso min: 14.53 Å2
Baniso -1Baniso -2Baniso -3
1--3.62 Å2-0 Å2-0 Å2
2---3.62 Å2-0 Å2
3---7.23 Å2
Refinement stepCycle: final / Resolution: 3→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12740 0 0 0 12740
Num. residues----1614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01213093
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.64217824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.59751599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80222.167720
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.489152012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4991583
X-RAY DIFFRACTIONr_chiral_restr0.1080.21681
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210302
LS refinement shellResolution: 3.004→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 134 -
Rwork0.362 2489 -
all-2623 -
obs--76.41 %
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)
11.820.23880.09190.2382-0.17360.5399-0.0746-0.17080.1843-0.01080.01630.0527-0.09370.12230.05830.0659-0.0401-0.02540.2137-0.0510.080127.502616.7104-0.7135
23.2508-0.88150.5951.34750.03341.8605-0.0977-0.1058-0.0564-0.20340.0755-0.05370.02350.13880.02220.064-0.03250.02620.15790.01560.082540.43914.6035-8.1096
31.28660.0146-0.43010.50540.40370.84280.0295-0.22510.206-0.0436-0.05310.0001-0.0282-0.13310.02360.02310.04780.0110.2891-0.06970.0562-24.110912.602419.722
42.00660.254-0.45750.0467-0.09010.6491-0.167-0.0085-0.0267-0.05460.0441-0.00140.1804-0.29590.12290.1018-0.10430.00850.3435-0.09210.0456-29.2543-0.13985.337
51.60830.4172-0.47880.18050.07960.9182-0.11120.3101-0.0601-0.02680.0214-0.016-0.0952-0.31770.08970.09640.0008-0.04020.2843-0.0750.0428.9451-34.4135-11.5735
61.0604-0.02741.41171.5009-0.6573.0568-0.1410.1374-0.13470.0610.03690.34870.113-0.34470.10410.1279-0.19020.17880.2998-0.24530.299522.3783-52.5228-3.5744
70.80080.68730.15590.8435-0.13040.3817-0.09870.0990.1379-0.12040.05270.1375-0.03660.02110.0460.1365-0.0043-0.02720.18660.01180.045372.0921-8.9944-30.0428
81.1770.77320.36610.7555-0.07680.6501-0.03110.0277-0.0903-0.0608-0.0188-0.05720.06920.15540.04990.04180.00320.03280.1595-0.01290.104282.5684-17.1164-15.9109
92.41892.0038-0.08594.34261.01570.4440.1088-0.28610.44210.4543-0.14590.47240.15110.05290.03710.10560.02160.04450.286-0.02550.0898.665111.61652.2395
103.22251.03760.77314.5432-1.24790.7235-0.12390.1617-0.0134-0.03640.1563-0.0279-0.0425-0.0135-0.03240.0660.01940.04920.18970.02540.157144.4377-29.0601-13.6213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 274
2X-RAY DIFFRACTION2B1 - 100
3X-RAY DIFFRACTION3D2 - 202
4X-RAY DIFFRACTION4E3 - 242
5X-RAY DIFFRACTION5F2 - 272
6X-RAY DIFFRACTION6G1 - 99
7X-RAY DIFFRACTION7H3 - 200
8X-RAY DIFFRACTION8J2 - 242
9X-RAY DIFFRACTION9P1 - 9
10X-RAY DIFFRACTION10Q1 - 9

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