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- PDB-7eeu: Human p53 core domain with hot spot mutation R282W in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7eeu
TitleHuman p53 core domain with hot spot mutation R282W in complex with the natural CDKN1A(p21) p53-response element and Arsenic
Components
  • CDKN1A(p21) anti-sense strand
  • CDKN1A(p21) sense strand
  • Cellular tumor antigen p53
KeywordsTRANSCRIPTION / DNA-binding domain / complex / DNA-bound / Arsenic-bound
Function / homology
Function and homology information


negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity ...negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / cellular response to actinomycin D / circadian behavior / positive regulation of programmed necrotic cell death / RUNX3 regulates CDKN1A transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / Regulation of TP53 Activity through Association with Co-factors / Urea cycle / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / hematopoietic progenitor cell differentiation / negative regulation of telomere maintenance via telomerase / 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 in response to DNA damage by p53 class mediator / replicative senescence / Transcriptional Regulation by VENTX / TFIID-class transcription factor complex binding / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / determination of adult lifespan / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / negative regulation of fibroblast proliferation / positive regulation of execution phase of apoptosis / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway / 14-3-3 protein binding / response to gamma radiation / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / DNA damage response, signal transduction by p53 class mediator / transcription initiation-coupled chromatin remodeling / molecular function activator activity / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / TP53 Regulates Metabolic Genes / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / mRNA 3'-UTR binding / Regulation of NF-kappa B signaling / protein tetramerization / molecular condensate scaffold activity / promoter-specific chromatin binding / Stabilization of p53 / negative regulation of cell growth / nucleotide-excision repair / G2/M Checkpoints / receptor tyrosine kinase binding / Autodegradation of the E3 ubiquitin ligase COP1 / cellular senescence / PML body / PKR-mediated signaling / positive regulation of miRNA transcription / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / transcription coactivator binding / intracellular protein localization / positive regulation of reactive oxygen species metabolic process / histone deacetylase binding
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 ...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 / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsXing, Y.F. / Lu, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81861130368 China
CitationJournal: To Be Published
Title: Human p53 core domain with hot spot mutation R282W in complex with the natural CDKN1A(p21) p53-response element and Arsenic
Authors: Xing, Y.F. / Lu, M.
History
DepositionMar 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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
E: Cellular tumor antigen p53
F: Cellular tumor antigen p53
G: Cellular tumor antigen p53
H: Cellular tumor antigen p53
I: CDKN1A(p21) sense strand
J: CDKN1A(p21) anti-sense strand
K: CDKN1A(p21) sense strand
L: CDKN1A(p21) anti-sense strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,50730
Polymers217,17312
Non-polymers1,33518
Water28816
1
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: Cellular tumor antigen p53
D: Cellular tumor antigen p53
I: CDKN1A(p21) sense strand
J: CDKN1A(p21) anti-sense strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,14814
Polymers108,5866
Non-polymers5618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Cellular tumor antigen p53
F: Cellular tumor antigen p53
G: Cellular tumor antigen p53
H: Cellular tumor antigen p53
K: CDKN1A(p21) sense strand
L: CDKN1A(p21) anti-sense strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,36016
Polymers108,5866
Non-polymers77410
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.815, 95.575, 99.646
Angle α, β, γ (deg.)89.620, 89.850, 75.790
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H
129I
229K
130J
230L

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
11SERSERLYSLYSAA95 - 2922 - 199
21SERSERLYSLYSBB95 - 2922 - 199
12SERSERLYSLYSAA95 - 2922 - 199
22SERSERLYSLYSCC95 - 2922 - 199
13SERSERLYSLYSAA95 - 2922 - 199
23SERSERLYSLYSDD95 - 2922 - 199
14SERSERLYSLYSAA95 - 2922 - 199
24SERSERLYSLYSEE95 - 2922 - 199
15SERSERLYSLYSAA96 - 2913 - 198
25SERSERLYSLYSFF96 - 2913 - 198
16SERSERLYSLYSAA95 - 2922 - 199
26SERSERLYSLYSGG95 - 2922 - 199
17SERSERLYSLYSAA95 - 2922 - 199
27SERSERLYSLYSHH95 - 2922 - 199
18SERSERLYSLYSBB95 - 2922 - 199
28SERSERLYSLYSCC95 - 2922 - 199
19SERSERLYSLYSBB95 - 2922 - 199
29SERSERLYSLYSDD95 - 2922 - 199
110SERSERLYSLYSBB95 - 2922 - 199
210SERSERLYSLYSEE95 - 2922 - 199
111SERSERLYSLYSBB96 - 2913 - 198
211SERSERLYSLYSFF96 - 2913 - 198
112SERSERLYSLYSBB95 - 2922 - 199
212SERSERLYSLYSGG95 - 2922 - 199
113SERSERLYSLYSBB95 - 2922 - 199
213SERSERLYSLYSHH95 - 2922 - 199
114SERSERLYSLYSCC95 - 2922 - 199
214SERSERLYSLYSDD95 - 2922 - 199
115SERSERLYSLYSCC95 - 2922 - 199
215SERSERLYSLYSEE95 - 2922 - 199
116SERSERLYSLYSCC96 - 2913 - 198
216SERSERLYSLYSFF96 - 2913 - 198
117SERSERLYSLYSCC95 - 2922 - 199
217SERSERLYSLYSGG95 - 2922 - 199
118SERSERLYSLYSCC95 - 2922 - 199
218SERSERLYSLYSHH95 - 2922 - 199
119SERSERLYSLYSDD95 - 2922 - 199
219SERSERLYSLYSEE95 - 2922 - 199
120SERSERLYSLYSDD96 - 2913 - 198
220SERSERLYSLYSFF96 - 2913 - 198
121SERSERLYSLYSDD95 - 2922 - 199
221SERSERLYSLYSGG95 - 2922 - 199
122SERSERLYSLYSDD95 - 2922 - 199
222SERSERLYSLYSHH95 - 2922 - 199
123SERSERLYSLYSEE96 - 2913 - 198
223SERSERLYSLYSFF96 - 2913 - 198
124SERSERLYSLYSEE95 - 2922 - 199
224SERSERLYSLYSGG95 - 2922 - 199
125SERSERLYSLYSEE95 - 2922 - 199
225SERSERLYSLYSHH95 - 2922 - 199
126SERSERLYSLYSFF96 - 2913 - 198
226SERSERLYSLYSGG96 - 2913 - 198
127SERSERLYSLYSFF96 - 2913 - 198
227SERSERLYSLYSHH96 - 2913 - 198
128SERSERLYSLYSGG95 - 2922 - 199
228SERSERLYSLYSHH95 - 2922 - 199
129DCDCDGDGII1 - 301 - 30
229DCDCDGDGKK1 - 301 - 30
130DCDCDGDGJJ1 - 301 - 30
230DCDCDGDGLL1 - 301 - 30

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 22534.598 Da / Num. of mol.: 8 / Mutation: R282W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli (E. coli) / References: UniProt: P04637

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DNA chain , 2 types, 4 molecules IKJL

#2: DNA chain CDKN1A(p21) sense strand


Mass: 9232.954 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain CDKN1A(p21) anti-sense strand


Mass: 9214.928 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 34 molecules

#4: Chemical
ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: As / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate, 0.1 M HEPES pH 8.0, 10% w/v PEG 4000, 2mM EDTA and 2mM As2O3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03314 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03314 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.739
11-h,-k,l20.261
ReflectionResolution: 2.88→46.32 Å / Num. obs: 52345 / % possible obs: 89.4 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.055 / Rrim(I) all: 0.107 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-2.993.90.5761802146140.9310.3360.6672.190.1
11.96-46.323.60.04226647460.9970.0260.0522.290

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J1Y

2j1y


Resolution: 2.9→45.39 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.991 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 2623 5.2 %RANDOM
Rwork0.2337 ---
obs0.2353 47968 84.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 225.87 Å2 / Biso mean: 82.75 Å2 / Biso min: 8.79 Å2
Baniso -1Baniso -2Baniso -3
1--86.45 Å221.77 Å2-7.02 Å2
2---60.64 Å29.07 Å2
3---147.09 Å2
Refinement stepCycle: final / Resolution: 2.9→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12482 2460 30 16 14988
Biso mean--111.05 59.55 -
Num. residues----1703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01815602
X-RAY DIFFRACTIONr_bond_other_d0.0070.0213282
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.80421598
X-RAY DIFFRACTIONr_angle_other_deg1.4813.00330652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45851575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.64722.432592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.376152151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.47915136
X-RAY DIFFRACTIONr_chiral_restr0.0790.22231
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02115925
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023647
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110670.1
12B110670.1
21A110170.09
22C110170.09
31A110870.1
32D110870.1
41A113710.07
42E113710.07
51A110190.09
52F110190.09
61A110420.09
62G110420.09
71A110010.11
72H110010.11
81B108970.1
82C108970.1
91B109000.11
92D109000.11
101B109950.1
102E109950.1
111B109960.09
112F109960.09
121B109050.1
122G109050.1
131B108270.12
132H108270.12
141C110640.09
142D110640.09
151C109720.1
152E109720.1
161C108900.1
162F108900.1
171C112340.08
172G112340.08
181C109940.1
182H109940.1
191D110530.11
192E110530.11
201D108660.1
202F108660.1
211D111500.1
212G111500.1
221D112010.1
222H112010.1
231E109620.1
232F109620.1
241E110000.1
242G110000.1
251E109570.11
252H109570.11
261F109090.1
262G109090.1
271F108460.11
272H108460.11
281G111270.1
282H111270.1
291I24290.03
292K24290.03
301J24460.06
302L24460.06
LS refinement shellResolution: 2.882→2.957 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 165 -
Rwork0.362 2785 -
all-2950 -
obs--66.34 %

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