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- PDB-3exl: Crystal Structure of a p53 Core Tetramer Bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3exl
TitleCrystal Structure of a p53 Core Tetramer Bound to DNA
Components
  • 5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'
  • 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'
  • mouse p53 core domain
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / Acetylation / Activator / Anti-oncogene / Apoptosis / Cell cycle / Covalent protein-RNA linkage / Cytoplasm / Disease mutation / DNA-binding / Endoplasmic reticulum / Metal-binding / Methylation / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation / Zinc / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Expression / Regulation of TP53 Activity through Acetylation / Transcriptional activation of cell cycle inhibitor p21 / Regulation of TP53 Activity through Association with Co-factors / RUNX3 regulates CDKN1A transcription / regulation of thymocyte apoptotic process / PI5P Regulates TP53 Acetylation / DNA Damage/Telomere Stress Induced Senescence / Stabilization of p53 ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Expression / Regulation of TP53 Activity through Acetylation / Transcriptional activation of cell cycle inhibitor p21 / Regulation of TP53 Activity through Association with Co-factors / RUNX3 regulates CDKN1A transcription / regulation of thymocyte apoptotic process / PI5P Regulates TP53 Acetylation / DNA Damage/Telomere Stress Induced Senescence / Stabilization of p53 / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / Regulation of TP53 Degradation / Oncogene Induced Senescence / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Ovarian tumor domain proteases / PKR-mediated signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of cellular senescence / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Ub-specific processing proteases / negative regulation of DNA biosynthetic process / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing 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 / embryo development ending in birth or egg hatching / 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 / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of leukocyte migration / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TFIID-class transcription factor complex binding / mitophagy / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / negative regulation of mitotic cell cycle / 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 / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / somitogenesis / positive regulation of cell cycle / type II interferon-mediated signaling pathway / regulation of neuron apoptotic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
Similarity search - Function
Immunoglobulin-like - #720 / 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 ...Immunoglobulin-like - #720 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / DNA / DNA (> 10) / Cellular tumor antigen p53
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMalecka, K.A.
CitationJournal: Oncogene / Year: 2009
Title: Crystal structure of a p53 core tetramer bound to DNA.
Authors: Malecka, K.A. / Ho, W.C. / Marmorstein, R.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999The complete crystallized DNA sequence is 5'-TTGAGCATGCTCGAGCATGCTCA-3'. The sequence in the ...The complete crystallized DNA sequence is 5'-TTGAGCATGCTCGAGCATGCTCA-3'. The sequence in the asymmetric unit is only a quarter of the complete sequence (TGCTC for chain C and GAGCA for chain D). The biological unit of tetramer is generated by applying to chains (A,C,D) (X, Y, Z+1; -X, Y, -Z; -X, Y, -Z+1) symmetry.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mouse p53 core domain
C: 5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'
D: 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6505
Polymers29,3953
Non-polymers2552
Water2,900161
1
A: mouse p53 core domain
C: 5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'
D: 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'
hetero molecules

A: mouse p53 core domain
C: 5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'
D: 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'
hetero molecules

A: mouse p53 core domain
C: 5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'
D: 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'
hetero molecules

A: mouse p53 core domain
C: 5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'
D: 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,59920
Polymers117,58112
Non-polymers1,0188
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)109.418, 68.103, 34.428
Angle α, β, γ (deg.)90.00, 104.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein mouse p53 core domain


Mass: 22383.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P02340

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain 5'-D(*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: p53 consensus sequence
#3: DNA chain 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'


Mass: 3653.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: p53 consensus sequence

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Non-polymers , 3 types, 163 molecules

#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 200 mM lithium citrate, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Lithium Citrate11
2PEG 335011
3Lithium Citrate12
4PEG 335012

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorDate: Apr 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→57.354 Å / Num. obs: 12509 / Redundancy: 4.9 % / Rsym value: 0.1 / Net I/σ(I): 14.7
Reflection shellHighest resolution: 2.2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.277

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→57.354 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.253 1246 9.9 %
Rwork0.202 10899 -
obs-12145 97 %
Solvent computationBsol: 43.798 Å2
Displacement parametersBiso max: 89.05 Å2 / Biso mean: 33.457 Å2 / Biso min: 14.78 Å2
Baniso -1Baniso -2Baniso -3
1-17.816 Å20 Å2-5.122 Å2
2---1.23 Å20 Å2
3----16.586 Å2
Refinement stepCycle: LAST / Resolution: 2.2→57.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 205 14 161 1897
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2831.5
X-RAY DIFFRACTIONc_scbond_it2.1422
X-RAY DIFFRACTIONc_mcangle_it2.0222
X-RAY DIFFRACTIONc_scangle_it3.0552.5
LS refinement shellHighest resolution: 2.2 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5flc_xplor_par.param

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