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- PDB-7eax: Crystal complex of p53-V272M and antimony ion -

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Basic information

Entry
Database: PDB / ID: 7eax
TitleCrystal complex of p53-V272M and antimony ion
ComponentsCellular tumor antigen p53
KeywordsANTITUMOR PROTEIN / tumor suppressor p53 / structural stabilization
Function / homology
Function and homology information


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 ...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 / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / circadian behavior / bone marrow development / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / negative regulation of DNA replication / 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 / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of release of cytochrome c from mitochondria / necroptotic process / Zygotic genome activation (ZGA) / positive regulation of execution phase of apoptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / replicative senescence / response to X-ray / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / mitophagy / cellular response to UV-C / positive regulation of RNA polymerase II transcription preinitiation complex assembly / hematopoietic stem cell differentiation / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chromosome organization / T cell proliferation involved in immune response / Pyroptosis / embryonic organ development / glial cell proliferation / viral process / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / type II interferon-mediated signaling pathway / somitogenesis / cellular response to actinomycin D / core promoter sequence-specific DNA binding / cellular response to glucose starvation / negative regulation of stem cell proliferation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / response to salt stress / cardiac muscle cell apoptotic process / mitotic G1 DNA damage checkpoint signaling / tumor necrosis factor-mediated signaling pathway / 14-3-3 protein binding / Regulation of TP53 Activity through Acetylation
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
Similarity search - Domain/homology
ANTIMONY (III) ION / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLu, M. / Tang, Y.
Funding support China, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81622002 China
National Natural Science Foundation of China (NSFC)81861130368 China
National Natural Science Foundation of China (NSFC)82073292 China
Other governmentShanghai Youth Talent Development Program (2017275) China
Other governmentShanghai Medical and Health Excellent Discipline Leader Development Plan (2018BR36) China
Other governmentShanghai Collaborative Innovation Center for Translational Medicine (TM201902) China
Other governmentFoundation of National Facility for Translational Medicine (Shanghai) (TMSK-2020-003) China
CitationJournal: Cell Rep / Year: 2022
Title: Repurposing antiparasitic antimonials to noncovalently rescue temperature-sensitive p53 mutations.
Authors: Tang, Y. / Song, H. / Wang, Z. / Xiao, S. / Xiang, X. / Zhan, H. / Wu, L. / Wu, J. / Xing, Y. / Tan, Y. / Liang, Y. / Yan, N. / Li, Y. / Li, J. / Wu, J. / Zheng, D. / Jia, Y. / Chen, Z. / ...Authors: Tang, Y. / Song, H. / Wang, Z. / Xiao, S. / Xiang, X. / Zhan, H. / Wu, L. / Wu, J. / Xing, Y. / Tan, Y. / Liang, Y. / Yan, N. / Li, Y. / Li, J. / Wu, J. / Zheng, D. / Jia, Y. / Chen, Z. / Li, Y. / Zhang, Q. / Zhang, J. / Zeng, H. / Tao, W. / Liu, F. / Wu, Y. / Lu, M.
History
DepositionMar 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: 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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,31212
Polymers87,5644
Non-polymers7498
Water1,11762
1
A: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0783
Polymers21,8911
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20 Å2
ΔGint-4 kcal/mol
Surface area10260 Å2
MethodPISA
2
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0783
Polymers21,8911
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20 Å2
ΔGint-3 kcal/mol
Surface area10200 Å2
MethodPISA
3
C: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0783
Polymers21,8911
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10190 Å2
MethodPISA
4
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0783
Polymers21,8911
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.876, 72.551, 85.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASNASNAA97 - 2882 - 193
21VALVALASNASNBB97 - 2882 - 193
12SERSERLEULEUAA96 - 2891 - 194
22SERSERLEULEUCC96 - 2891 - 194
13VALVALASNASNAA97 - 2882 - 193
23VALVALASNASNDD97 - 2882 - 193
14VALVALASNASNBB97 - 2882 - 193
24VALVALASNASNCC97 - 2882 - 193
15VALVALLEULEUBB97 - 2892 - 194
25VALVALLEULEUDD97 - 2892 - 194
16VALVALASNASNCC97 - 2882 - 193
26VALVALASNASNDD97 - 2882 - 193

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Cellular tumor antigen p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 21890.885 Da / Num. of mol.: 4 / Mutation: V272M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P04637
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SB / ANTIMONY (III) ION


Mass: 121.760 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sb / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 10% w/v PEG3350 and 0.2M Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.609
11-h,-k,l20.391
ReflectionResolution: 2.55→42.53 Å / Num. obs: 26974 / % possible obs: 98.1 % / Redundancy: 3.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.075 / Rrim(I) all: 0.141 / Χ2: 1 / Net I/σ(I): 8.6
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3329 / CC1/2: 0.838 / Rpim(I) all: 0.389 / Rrim(I) all: 0.743 / Χ2: 1.01 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OCJ

2ocj


Resolution: 2.55→42.53 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.712 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 1264 4.7 %RANDOM
Rwork0.2063 ---
obs0.2076 25693 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.96 Å2 / Biso mean: 44.372 Å2 / Biso min: 12.69 Å2
Baniso -1Baniso -2Baniso -3
1--43.9 Å2-0 Å20.18 Å2
2--67.71 Å20 Å2
3----23.82 Å2
Refinement stepCycle: final / Resolution: 2.55→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 8 62 6154
Biso mean--49.2 30.29 -
Num. residues----774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136311
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175646
X-RAY DIFFRACTIONr_angle_refined_deg1.271.6668551
X-RAY DIFFRACTIONr_angle_other_deg1.0561.57313127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.90220.055362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.995151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4891569
X-RAY DIFFRACTIONr_chiral_restr0.0360.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021378
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A59160.03
12B59160.03
21A59310.05
22C59310.05
31A58950.04
32D58950.04
41B59330.05
42C59330.05
51B59740.04
52D59740.04
61C58630.04
62D58630.04
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 107 -
Rwork0.294 1886 -
all-1993 -
obs--99.2 %

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