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- PDB-2h1l: The Structure of the Oncoprotein SV40 Large T Antigen and p53 Tum... -

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Basic information

Entry
Database: PDB / ID: 2h1l
TitleThe Structure of the Oncoprotein SV40 Large T Antigen and p53 Tumor Suppressor Complex
Components
  • Cellular tumor antigen p53P53
  • Large T antigenLarge tumor antigen
KeywordsVIRAL PROTEIN / p53 Loop-3 conformation change
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / 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 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / 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 / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / 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 / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / DNA unwinding involved in DNA replication / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / DNA replication origin binding / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation
Similarity search - Function
Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding ...Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / Immunoglobulin-like - #720 / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / DnaJ domain / 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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / p53-like transcription factor, DNA-binding / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Large T antigen / Cellular tumor antigen p53 / Large T antigen / Cellular tumor antigen p53
Similarity search - Component
Biological speciesSimian virus 40
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsLilyestrom, W. / Klein, M.G. / Chen, X.S.
CitationJournal: Genes Dev. / Year: 2006
Title: Crystal structure of SV40 large T-antigen bound to p53: interplay between a viral oncoprotein and a cellular tumor suppressor.
Authors: Lilyestrom, W. / Klein, M.G. / Zhang, R. / Joachimiak, A. / Chen, X.S.
History
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_biol / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large T antigen
B: Large T antigen
C: Large T antigen
D: Large T antigen
E: Large T antigen
F: Large T antigen
G: Large T antigen
H: Large T antigen
I: Large T antigen
J: Large T antigen
K: Large T antigen
L: Large T antigen
M: Cellular tumor antigen p53
N: Cellular tumor antigen p53
O: Cellular tumor antigen p53
P: Cellular tumor antigen p53
Q: Cellular tumor antigen p53
R: Cellular tumor antigen p53
S: Cellular tumor antigen p53
T: Cellular tumor antigen p53
U: Cellular tumor antigen p53
V: Cellular tumor antigen p53
W: Cellular tumor antigen p53
X: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)786,95048
Polymers785,38024
Non-polymers1,57024
Water0
1
A: Large T antigen
B: Large T antigen
C: Large T antigen
D: Large T antigen
E: Large T antigen
F: Large T antigen
M: Cellular tumor antigen p53
N: Cellular tumor antigen p53
O: Cellular tumor antigen p53
P: Cellular tumor antigen p53
Q: Cellular tumor antigen p53
R: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,47524
Polymers392,69012
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36530 Å2
ΔGint-247 kcal/mol
Surface area135910 Å2
MethodPISA
2
G: Large T antigen
H: Large T antigen
I: Large T antigen
J: Large T antigen
K: Large T antigen
L: Large T antigen
S: Cellular tumor antigen p53
T: Cellular tumor antigen p53
U: Cellular tumor antigen p53
V: Cellular tumor antigen p53
W: Cellular tumor antigen p53
X: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,47524
Polymers392,69012
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35850 Å2
ΔGint-164 kcal/mol
Surface area135630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.019, 182.718, 262.061
Angle α, β, γ (deg.)90.00, 92.08, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a single hexamer containing six LT and six p53 molecules. There are two such hexamers in the asu. The first contains chains A-F and M-R. The is composed of chains G-L and S-X.

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Components

#1: Protein
Large T antigen / Large tumor antigen


Mass: 42645.426 Da / Num. of mol.: 12 / Fragment: Helicase Domain, residues 260-627
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: PolyomavirusPolyomaviridae / Gene: Gene A / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: Q9DH70, UniProt: P03070*PLUS
#2: Protein
Cellular tumor antigen p53 / P53 / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 22802.936 Da / Num. of mol.: 12 / Fragment: DNA Binding Domain, residues 92-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: p53 / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: Q9NP68, UniProt: P04637*PLUS
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn

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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: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 5.4% PEG 4000, 73mM Mops Buffer, 22mM Lithium Sulfate, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.16→20 Å / Num. obs: 204669 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rsym value: 0.069 / Net I/σ(I): 30.3
Reflection shellResolution: 3.16→3.27 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 204669 / Rsym value: 0.398 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
HKL-2000data reduction
MOLREPphasing
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SVM

1svm


Resolution: 3.16→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3081 9027 -RANDOM
Rwork0.2614 ---
all0.069 ---
obs0.069 204669 97.3 %-
Displacement parametersBiso mean: 75.3 Å2
Refinement stepCycle: LAST / Resolution: 3.16→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53896 0 24 0 53920
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012744
X-RAY DIFFRACTIONc_angle_deg1.21289
LS refinement shellResolution: 3.16→3.27 Å / Num. reflection obs: 19180
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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