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- PDB-2x0v: STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO 4-(trifluo... -

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Basic information

Entry
Database: PDB / ID: 2x0v
TitleSTRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO 4-(trifluoromethyl)benzene-1,2-diamine
ComponentsCELLULAR TUMOR ANTIGEN P53
KeywordsCELL CYCLE / HOST-VIRUS INTERACTION / TRANSCRIPTION REGULATION / TRANSCRIPTION FACTOR / LI-FRAUMENI DRUG DISCOVERY / SURFACE CREVICE / TUMOR SUPPRESSOR / PROTEIN STABILIZATION / TRANSCRIPTION / METAL BINDING / CANCER / APOPTOSIS
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 / negative regulation of mitophagy / mRNA transcription / circadian behavior / bone marrow development / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of DNA damage response, signal transduction by p53 class mediator / 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 / : / 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 DNA replication / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / negative regulation of telomere maintenance via telomerase / necroptotic process / positive regulation of release of cytochrome c from mitochondria / Zygotic genome activation (ZGA) / Association of TriC/CCT with target proteins during biosynthesis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / T cell proliferation involved in immune response / rRNA transcription / 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 / positive regulation of execution phase of apoptosis / Transcriptional Regulation by VENTX / general transcription initiation factor binding / replicative senescence / cellular response to actinomycin D / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to UV-C / neuroblast proliferation / hematopoietic stem cell differentiation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / response to X-ray / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / chromosome organization / viral process / Pyroptosis / embryonic organ development / cis-regulatory region sequence-specific DNA binding / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / : / cellular response to glucose starvation / mitophagy / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / tumor necrosis factor-mediated signaling pathway / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation / gastrulation / MDM2/MDM4 family protein binding / response to salt stress / 14-3-3 protein binding
Similarity search - Function
Immunoglobulin-like - #720 / 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 ...Immunoglobulin-like - #720 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
4-(TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBasse, N. / Kaar, J.L. / Joerger, A.C. / Fersht, A.R.
Citation
Journal: Chem.Biol. / Year: 2010
Title: Toward the Rational Design of P53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant.
Authors: Basse, N. / Kaar, J.L. / Settanni, G. / Joerger, A.C. / Rutherford, T.J. / Fersht, A.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structural Basis for Understanding Oncogenic P53 Mutations and Designing Rescue Drugs.
Authors: Joerger, A.C. / Ang, H.C. / Fersht, A.R.
History
DepositionDec 17, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLULAR TUMOR ANTIGEN P53
B: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5456
Polymers49,0622
Non-polymers4834
Water10,305572
1
A: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5962
Polymers24,5311
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9484
Polymers24,5311
Non-polymers4183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.226, 71.088, 105.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CELLULAR TUMOR ANTIGEN P53 / TUMOR SUPPRESSOR P53 / PHOSPHOPROTEIN P53 / ANTIGEN NY-CO-13 / P53


Mass: 24530.811 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 94-312 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04637
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-X0V / 4-(TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE


Mass: 176.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7F3N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 133 TO LEU ENGINEERED RESIDUE IN CHAIN A, VAL 203 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, MET 133 TO LEU ENGINEERED RESIDUE IN CHAIN A, VAL 203 TO ALA ENGINEERED RESIDUE IN CHAIN A, TYR 220 TO CYS ENGINEERED RESIDUE IN CHAIN A, ASN 239 TO TYR ENGINEERED RESIDUE IN CHAIN A, ASN 268 TO ASP ENGINEERED RESIDUE IN CHAIN B, MET 133 TO LEU ENGINEERED RESIDUE IN CHAIN B, VAL 203 TO ALA ENGINEERED RESIDUE IN CHAIN B, TYR 220 TO CYS ENGINEERED RESIDUE IN CHAIN B, ASN 239 TO TYR ENGINEERED RESIDUE IN CHAIN B, ASN 268 TO ASP

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19 % PEG 4000, 5 ...Details: SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19 % PEG 4000, 5 MM DTT. SOAKING BUFFER: SATURATED SOLUTION OF SMALL MOLECULE LIGAND IN 100 MM HEPES PH 7.2, 10 MM SODIUM PHOSPHATE PH 7.2, 19 % PEG 4000, 20 % GLYCEROL, 150 MM KCL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.8→41.1 Å / Num. obs: 45419 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.5 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J1X

2j1x


Resolution: 1.8→24.03 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 17.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 4276 5 %
Rwork0.1622 --
obs0.1635 86003 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.271 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.3156 Å2-0 Å2-0 Å2
2---3.2917 Å20 Å2
3----2.0238 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 26 572 3637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053183
X-RAY DIFFRACTIONf_angle_d0.9044326
X-RAY DIFFRACTIONf_dihedral_angle_d13.6111197
X-RAY DIFFRACTIONf_chiral_restr0.065480
X-RAY DIFFRACTIONf_plane_restr0.004563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.27461700.20572636X-RAY DIFFRACTION94
1.8205-1.84190.24911790.20272655X-RAY DIFFRACTION98
1.8419-1.86430.2251540.19152685X-RAY DIFFRACTION97
1.8643-1.88790.2171610.1842686X-RAY DIFFRACTION98
1.8879-1.91280.23331260.17732744X-RAY DIFFRACTION97
1.9128-1.93890.18051510.16512671X-RAY DIFFRACTION98
1.9389-1.96660.21631540.17322741X-RAY DIFFRACTION97
1.9666-1.9960.17391070.17352713X-RAY DIFFRACTION98
1.996-2.02720.18461400.17112753X-RAY DIFFRACTION97
2.0272-2.06040.19391190.16342728X-RAY DIFFRACTION99
2.0604-2.09590.22221700.16572707X-RAY DIFFRACTION97
2.0959-2.1340.18911660.16062706X-RAY DIFFRACTION99
2.134-2.1750.20071420.15732708X-RAY DIFFRACTION98
2.175-2.21930.19021600.1432718X-RAY DIFFRACTION98
2.2193-2.26760.15571220.15342780X-RAY DIFFRACTION99
2.2676-2.32030.17651470.14812702X-RAY DIFFRACTION98
2.3203-2.37830.1651250.15282748X-RAY DIFFRACTION98
2.3783-2.44250.17871460.14982765X-RAY DIFFRACTION99
2.4425-2.51430.2291440.1562734X-RAY DIFFRACTION99
2.5143-2.59540.19861300.1592772X-RAY DIFFRACTION99
2.5954-2.6880.18331470.15972748X-RAY DIFFRACTION99
2.688-2.79550.22151600.1572688X-RAY DIFFRACTION99
2.7955-2.92250.16331260.15822780X-RAY DIFFRACTION99
2.9225-3.07630.15651480.13972724X-RAY DIFFRACTION99
3.0763-3.26860.16081170.14672804X-RAY DIFFRACTION99
3.2686-3.52020.16521590.13882724X-RAY DIFFRACTION99
3.5202-3.87320.16581440.14472751X-RAY DIFFRACTION99
3.8732-4.43060.12451220.14142736X-RAY DIFFRACTION98
4.4306-5.57060.14541250.14512732X-RAY DIFFRACTION98
5.5706-24.03250.20231150.19952688X-RAY DIFFRACTION95

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