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- PDB-4rp7: Structure of the amyloid-forming segment TIITLE from p53 (residue... -

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Basic information

Entry
Database: PDB / ID: 4rp7
TitleStructure of the amyloid-forming segment TIITLE from p53 (residues 253-258)
ComponentsTIITLE hexapeptide segment from p53
KeywordsPROTEIN FIBRIL / p53 / amyloid / fibril / amyloid-like protofibril / p53 aggregates / polymer / transcription factor / oncogene / cancer / p53 mutant
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 / T cell proliferation involved in immune response / 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 / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / 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 / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / cardiac muscle cell apoptotic process / response to salt stress / transcription initiation-coupled chromatin remodeling / mitotic G1 DNA damage checkpoint signaling / 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
Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.576 Å
AuthorsSoriaga, A.B. / Soragni, A. / Eisenberg, D.
CitationJournal: Cancer Cell / Year: 2016
Title: A Designed Inhibitor of p53 Aggregation Rescues p53 Tumor Suppression in Ovarian Carcinomas.
Authors: Soragni, A. / Janzen, D.M. / Johnson, L.M. / Lindgren, A.G. / Thai-Quynh Nguyen, A. / Tiourin, E. / Soriaga, A.B. / Lu, J. / Jiang, L. / Faull, K.F. / Pellegrini, M. / Memarzadeh, S. / Eisenberg, D.S.
History
DepositionOct 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
Z: TIITLE hexapeptide segment from p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7542
Polymers6891
Non-polymers651
Water362
1
Z: TIITLE hexapeptide segment from p53
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)4,52512
Polymers4,1336
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_585x,y+3,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
crystal symmetry operation4_566-x+1/2,y+3/2,-z+11
crystal symmetry operation4_576-x+1/2,y+5/2,-z+11
Unit cell
Length a, b, c (Å)43.018, 4.849, 19.774
Angle α, β, γ (deg.)90.00, 92.12, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a pair of beta sheets with the side chains interdigitating between the sheets. One sheet is constructed from unit cell translations along the "b" direction (i.e. X,Y+1,Z; X,Y+2,Z; X,Y+3,Z; etc.). The other sheet is constructed from symmetry operators -X+1/2,Y+1/2,-Z+1; -X+1/2,Y+3/2,-Z+1; -X+1/2,Y+5/2,-Z+1; etc.).

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Components

#1: Protein/peptide TIITLE hexapeptide segment from p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 688.810 Da / Num. of mol.: 1 / Fragment: UNP residues 253-258 / Source method: obtained synthetically / Details: TIITLE(residues 253-258) from p53, synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P04637
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 1.5 Å3/Da / Density % sol: 17.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: reservoir contained 0.01 M zinc chloride, 0.1 M MES buffer pH 6, and 20% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.576→21.494 Å / Num. all: 636 / Num. obs: 636 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.91
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.12 / % possible all: 87.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.576→21.494 Å / SU ML: 0.1 / σ(F): 1.43 / Phase error: 15.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 65 10.24 %RANDOM
Rwork0.1637 ---
all0.1666 635 --
obs0.1666 635 93.38 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4068 Å2-0 Å2-0.819 Å2
2---0.0323 Å20 Å2
3---2.1936 Å2
Refinement stepCycle: LAST / Resolution: 1.576→21.494 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms48 0 1 2 51
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00947
X-RAY DIFFRACTIONf_angle_d1.86164
X-RAY DIFFRACTIONf_dihedral_angle_d10.55717
X-RAY DIFFRACTIONf_chiral_restr0.07211
X-RAY DIFFRACTIONf_plane_restr0.0077
LS refinement shellHighest resolution: 1.576 Å
RfactorNum. reflection% reflection
Rfree0.1925 65 -
Rwork0.1637 570 -
obs--93 %
Refinement TLS params.Method: refined / Origin x: 10.525 Å / Origin y: -0.1582 Å / Origin z: 3.9867 Å
111213212223313233
T0.0284 Å20.0055 Å20.0058 Å2-0.0494 Å2-0.0102 Å2--0.029 Å2
L0.0034 °20.0063 °20.0031 °2-0.2021 °2-0.0919 °2--0.0378 °2
S0.0075 Å °-0.0003 Å °-0.0248 Å °-0.0899 Å °0.0437 Å °-0.0012 Å °-0.0422 Å °0.1216 Å °0.0477 Å °
Refinement TLS groupSelection details: all

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