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- PDB-6rz3: Crystal structure of a complex between the DNA-binding domain of ... -

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Basic information

Entry
Database: PDB / ID: 6rz3
TitleCrystal structure of a complex between the DNA-binding domain of p53 and the carboxyl-terminal conserved region of iASPP
Components
  • Cellular tumor antigen p53
  • RelA-associated inhibitor
KeywordsANTITUMOR PROTEIN / Complex / p53 / iASPP
Function / homology
Function and homology information


hair cycle / multicellular organismal-level homeostasis / cardiac right ventricle morphogenesis / embryonic camera-type eye development / ventricular cardiac muscle tissue development / negative regulation of helicase 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 ...hair cycle / multicellular organismal-level homeostasis / cardiac right ventricle morphogenesis / embryonic camera-type eye development / ventricular cardiac muscle tissue development / negative regulation of helicase 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 / 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 / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / regulation of fibroblast apoptotic process / cellular response to actinomycin D / germ cell nucleus / bone marrow development / circadian behavior / T cell proliferation involved in immune response / positive regulation of programmed necrotic cell death / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / : / RUNX3 regulates CDKN1A transcription / TP53 Regulates Transcription of Death Receptors and Ligands / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Activation of PUMA and translocation to mitochondria / mRNA transcription / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of neuroblast proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / thymocyte apoptotic process / ER overload response / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / B cell lineage commitment / entrainment of circadian clock by photoperiod / negative regulation of DNA replication / negative regulation of mitophagy / Zygotic genome activation (ZGA) / Association of TriC/CCT with target proteins during biosynthesis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TFIID-class transcription factor complex binding / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of reactive oxygen species metabolic process / rRNA transcription / Transcriptional Regulation by VENTX / cellular response to UV-C / viral process / replicative senescence / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / general transcription initiation factor binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Pyroptosis / chromosome organization / positive regulation of execution phase of apoptosis / embryonic organ development / hematopoietic stem cell differentiation / type II interferon-mediated signaling pathway / response to X-ray / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / hematopoietic progenitor cell differentiation / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / glial cell proliferation / cellular response to glucose starvation / negative regulation of fibroblast proliferation / mitophagy / intercellular bridge / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / cardiac muscle contraction / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of proteolysis / response to salt stress / mitotic G1 DNA damage checkpoint signaling
Similarity search - Function
RelA-associated inhibitor / RelA-associated inhibitor, SH3 domain / Variant SH3 domain / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / : / p53 family signature. / p53, tetramerisation domain ...RelA-associated inhibitor / RelA-associated inhibitor, SH3 domain / Variant SH3 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 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Cellular tumor antigen p53 / RelA-associated inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.23 Å
AuthorsChen, S. / Ren, J. / Jones, E.Y. / Lu, X.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: iASPP mediates p53 selectivity through a modular mechanism fine-tuning DNA recognition.
Authors: Chen, S. / Wu, J. / Zhong, S. / Li, Y. / Zhang, P. / Ma, J. / Ren, J. / Tan, Y. / Wang, Y. / Au, K.F. / Siebold, C. / Bond, G.L. / Chen, Z. / Lu, M. / Jones, E.Y. / Lu, X.
History
DepositionJun 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: RelA-associated inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8583
Polymers51,7922
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.090, 71.090, 255.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 25660.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04637
#2: Protein RelA-associated inhibitor / Inhibitor of ASPP protein / Protein iASPP / NFkB-interacting protein 1 / PPP1R13B-like protein


Mass: 26131.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R13L, IASPP, NKIP1, PPP1R13BL, RAI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WUF5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn
Has ligand of interestN

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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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 18% (w/v) polyethylene glycol 3350, 0.18 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 4.23→30 Å / Num. obs: 4819 / % possible obs: 93.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 8.3
Reflection shellResolution: 4.23→4.4 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 329 / % possible all: 94.7
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VGE, 2XWR

2vge

2xwr


Resolution: 4.23→29.8 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.888 / SU B: 160.302 / SU ML: 0.848 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.063
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2919 473 9.8 %RANDOM
Rwork0.2429 ---
obs0.2474 4346 93.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 378.53 Å2 / Biso mean: 195.602 Å2 / Biso min: 127.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å20 Å2
2--2.36 Å20 Å2
3----4.71 Å2
Refinement stepCycle: final / Resolution: 4.23→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 1 0 2867
Biso mean--210.61 --
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192940
X-RAY DIFFRACTIONr_bond_other_d0.0010.022655
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9414000
X-RAY DIFFRACTIONr_angle_other_deg0.72936112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.685366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11523.214140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35615452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8481524
X-RAY DIFFRACTIONr_chiral_restr0.0750.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02708
LS refinement shellResolution: 4.232→4.341 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 39 -
Rwork0.381 290 -
all-329 -
obs--92.16 %
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)
10.5578-1.0587-0.32123.185-0.04322.3267-0.0471-0.306-0.06460.0919-0.06730.3191-0.2077-0.10860.11440.1426-0.019-0.02040.9105-0.13820.059829.43851.950922.7779
20.6987-1.41640.46143.4394-0.44740.8517-0.0601-0.1233-0.0446-0.06080.05640.0478-0.0632-0.00210.00370.3795-0.08050.01270.86130.25250.079151.723129.590616.7486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 291
2X-RAY DIFFRACTION2B657 - 823

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