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- PDB-7dhy: Arsenic-bound p53 DNA-binding domain mutant G245S -

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Basic information

Entry
Database: PDB / ID: 7dhy
TitleArsenic-bound p53 DNA-binding domain mutant G245S
ComponentsCellular tumor antigen p53P53
KeywordsTRANSCRIPTION / tumour suppressor / transcription factor
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 / 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 / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / positive regulation of execution phase of apoptosis / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of cardiac muscle cell apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / T cell proliferation involved in immune response / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / rRNA transcription / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / general transcription initiation factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / chromosome organization / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / cellular response to actinomycin D / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / gastrulation / negative regulation of fibroblast proliferation / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription initiation-coupled chromatin remodeling / 14-3-3 protein binding / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation / 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
Similarity search - Domain/homology
ARSENIC / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChen, S. / Lu, M.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0506200 China
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
CitationJournal: Cancer Cell / Year: 2021
Title: Arsenic Trioxide Rescues Structural p53 Mutations through a Cryptic Allosteric Site.
Authors: Chen, S. / Wu, J.L. / Liang, Y. / Tang, Y.G. / Song, H.X. / Wu, L.L. / Xing, Y.F. / Yan, N. / Li, Y.T. / Wang, Z.Y. / Xiao, S.J. / Lu, X. / Chen, S.J. / Lu, M.
History
DepositionNov 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)91,44420
Polymers90,1424
Non-polymers1,30216
Water9,314517
1
A: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6763
Polymers22,5361
Non-polymers1402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9980 Å2
MethodPISA
2
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9526
Polymers22,5361
Non-polymers4175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10380 Å2
MethodPISA
3
C: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7684
Polymers22,5361
Non-polymers2323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9860 Å2
MethodPISA
4
D: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0487
Polymers22,5361
Non-polymers5136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.109, 68.243, 83.621
Angle α, β, γ (deg.)90.000, 90.030, 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: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASNASNAA97 - 2884 - 195
21VALVALASNASNBB97 - 2884 - 195
12VALVALASNASNAA97 - 2884 - 195
22VALVALASNASNCC97 - 2884 - 195
13VALVALASNASNAA97 - 2884 - 195
23VALVALASNASNDD97 - 2884 - 195
14SERSERASNASNBB96 - 2883 - 195
24SERSERASNASNCC96 - 2883 - 195
15SERSERASNASNBB96 - 2883 - 195
25SERSERASNASNDD96 - 2883 - 195
16SERSERLEULEUCC96 - 2893 - 196
26SERSERLEULEUDD96 - 2893 - 196

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cellular tumor antigen p53 / P53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 22535.609 Da / Num. of mol.: 4 / Mutation: G245S
Source method: isolated from a genetically manipulated source
Details: G245S / Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli (E. coli) / References: UniProt: P04637

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Non-polymers , 5 types, 533 molecules

#2: Chemical
ChemComp-ARS / ARSENIC / Arsenic


Mass: 74.922 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: As / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris (pH 8.0-8.5), 20% (w/v) PEG 8000, 0.2 M Li2SO4, 2 mM EDTA, and 2 mM As2O3
PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.657
11-h,-k,l20.343
ReflectionResolution: 2.15→50 Å / Num. obs: 41923 / % possible obs: 94.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.7
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 3334 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J1Y

2j1y


Resolution: 2.15→48.21 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.278 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.044
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2007 5.1 %RANDOM
Rwork0.1872 ---
obs0.1888 37578 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 139 Å2 / Biso mean: 37.004 Å2 / Biso min: 13.36 Å2
Baniso -1Baniso -2Baniso -3
1--22.7 Å20 Å2-7.7 Å2
2--32.45 Å20 Å2
3----9.75 Å2
Refinement stepCycle: final / Resolution: 2.15→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6114 0 55 517 6686
Biso mean--47.9 36.22 -
Num. residues----777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196364
X-RAY DIFFRACTIONr_bond_other_d0.0050.025891
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9688617
X-RAY DIFFRACTIONr_angle_other_deg1.0013.00313560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9075784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01822.423293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.966151051
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5911569
X-RAY DIFFRACTIONr_chiral_restr0.0640.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217182
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021495
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A113680.07
12B113680.07
21A111840.08
22C111840.08
31A112610.08
32D112610.08
41B113060.08
42C113060.08
51B112940.08
52D112940.08
61C112700.09
62D112700.09
LS refinement shellResolution: 2.15→2.205 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.338 189 -
Rwork0.274 2650 -
obs--91.55 %
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)
12.4136-0.26611.0720.0488-0.13490.65090.03230.0320.00860.0341-0.03790.01950.0507-0.00260.00570.1193-0.03950.06160.1355-0.01210.0331164.289-70.012151.7518
21.48010.00080.3170.0111-0.07720.614-0.0345-0.04720.0117-0.00550.0024-0.00570.01550.00710.03210.0993-0.00970.09110.0805-0.00430.0855167.9971-70.556410.938
31.80750.7091-0.40.2962-0.18780.2156-0.07560.19560.0639-0.0220.10480.03920.0065-0.0152-0.02920.0865-0.01660.05910.1380.01790.0522130.2567-61.724551.6361
40.62020.1181-0.08510.10790.0140.4107-0.008-0.00040.0188-0.0058-0.0008-0.04880.0143-0.06470.00880.0845-0.00320.07040.0926-0.00590.0883133.5437-62.43188.9408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A97 - 289
2X-RAY DIFFRACTION2B96 - 291
3X-RAY DIFFRACTION3C96 - 289
4X-RAY DIFFRACTION4D96 - 289

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