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- PDB-4rp6: Structure of the amyloid-forming segment LTIITLE from p53 (residu... -

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Basic information

Entry
Database: PDB / ID: 4rp6
TitleStructure of the amyloid-forming segment LTIITLE from p53 (residues 252-258)
ComponentsLTIITLE heptapeptide 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 / 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
Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Z: LTIITLE heptapeptide segment from p53


Theoretical massNumber of molelcules
Total (without water)8021
Polymers8021
Non-polymers00
Water362
1
Z: LTIITLE heptapeptide segment from p53
x 6


Theoretical massNumber of molelcules
Total (without water)4,8126
Polymers4,8126
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation1_765x+2,y+1,z1
Unit cell
Length a, b, c (Å)4.811, 12.599, 21.340
Angle α, β, γ (deg.)86.59, 89.29, 79.15
Int Tables number1
Space group name H-MP1
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 "a" direction (i.e. X+1,Y,Z X+2,Y,Z X+3,Y,Z, etc.). The other sheet is constructed from symmetry operators X,Y+1,Z; X+1,Y+1,Z; X+2,Y+1,Z, etc.).

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Components

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


Mass: 801.968 Da / Num. of mol.: 1 / Fragment: UNP residues 252-258 / Source method: obtained synthetically / Details: LTIITLE(residues 252-258) from p53, synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P04637
#2: Water ChemComp-HOH / 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: 1.58 Å3/Da / Density % sol: 22.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: reservoir contained 0.1 M Tris buffer pH 8.5 and 20% ethanol, 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: 1.703→21.302 Å / Num. all: 512 / Num. obs: 512 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.6
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 11.6 / % possible all: 91.4

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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: 1.703→21.302 Å / SU ML: 0.06 / σ(F): 2.14 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 50 9.86 %RANDOM
Rwork0.1626 ---
all0.1655 507 --
obs0.1655 507 93.72 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.131 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4505 Å2-0.2078 Å20.5956 Å2
2--0.3869 Å2-3.0866 Å2
3----1.8374 Å2
Refinement stepCycle: LAST / Resolution: 1.703→21.302 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms56 0 0 2 58
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761
X-RAY DIFFRACTIONf_angle_d1.0885
X-RAY DIFFRACTIONf_dihedral_angle_d18.34624
X-RAY DIFFRACTIONf_chiral_restr0.06115
X-RAY DIFFRACTIONf_plane_restr0.0039
LS refinement shellHighest resolution: 1.703 Å
RfactorNum. reflection% reflection
Rfree0.1919 50 -
Rwork0.1626 457 -
obs--94 %
Refinement TLS params.Method: refined / Origin x: 0.1185 Å / Origin y: 6.8484 Å / Origin z: 9.0224 Å
111213212223313233
T0.0582 Å20.0099 Å20.0029 Å2-0.075 Å20.009 Å2--0.0849 Å2
L2.3157 °2-0.4063 °2-1.1355 °2-4.0221 °21.8148 °2--4.8813 °2
S0.0087 Å °-0.0689 Å °-0.0102 Å °0.1493 Å °0.2397 Å °-0.0164 Å °-0.1178 Å °0.0395 Å °-0.1915 Å °
Refinement TLS groupSelection details: all

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