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- PDB-9gfo: iASPP-CTD fusion to p63 peptide -

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Basic information

Entry
Database: PDB / ID: 9gfo
TitleiASPP-CTD fusion to p63 peptide
ComponentsTumor protein 63,RelA-associated inhibitor
KeywordsTRANSCRIPTION / tp63 / alternative splicing / iASPP / PPP1R13L
Function / homology
Function and homology information


multicellular organismal-level homeostasis / ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / negative regulation of mesoderm development / prostatic bud formation / female genitalia morphogenesis / cardiac right ventricle morphogenesis / embryonic camera-type eye development ...multicellular organismal-level homeostasis / ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / negative regulation of mesoderm development / prostatic bud formation / female genitalia morphogenesis / cardiac right ventricle morphogenesis / embryonic camera-type eye development / hair cycle / positive regulation of keratinocyte proliferation / establishment of planar polarity / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / negative regulation of keratinocyte differentiation / polarized epithelial cell differentiation / negative regulation of intracellular estrogen receptor signaling pathway / proximal/distal pattern formation / positive regulation of fibroblast apoptotic process / ventricular cardiac muscle tissue development / skin morphogenesis / positive regulation of cell cycle G1/S phase transition / cranial skeletal system development / sympathetic nervous system development / post-anal tail morphogenesis / embryonic forelimb morphogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / embryonic hindlimb morphogenesis / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / hair follicle morphogenesis / WW domain binding / regulation of epidermal cell division / positive regulation of Notch signaling pathway / TP53 Regulates Transcription of Caspase Activators and Caspases / positive regulation of stem cell proliferation / epithelial cell development / odontogenesis of dentin-containing tooth / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / negative regulation of cellular senescence / keratinocyte proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Pyroptosis / establishment of skin barrier / positive regulation of osteoblast differentiation / intercellular bridge / keratinocyte differentiation / cardiac muscle contraction / Notch signaling pathway / MDM2/MDM4 family protein binding / positive regulation of apoptotic signaling pathway / post-embryonic development / stem cell proliferation / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / determination of adult lifespan / TP53 Regulates Metabolic Genes / positive regulation of cell differentiation / protein tetramerization / promoter-specific chromatin binding / multicellular organism growth / negative regulation of inflammatory response / transcription corepressor activity / cellular senescence / p53 binding / cell junction / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / spermatogenesis / transcription by RNA polymerase II / damaged DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / dendrite / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RelA-associated inhibitor / RelA-associated inhibitor, SH3 domain / Tumour protein p63, SAM domain / Variant SH3 domain / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family ...RelA-associated inhibitor / RelA-associated inhibitor, SH3 domain / Tumour protein p63, SAM domain / Variant SH3 domain / 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 / SAM domain (Sterile alpha motif) / p53-like transcription factor, DNA-binding / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / 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
RelA-associated inhibitor / Tumor protein 63
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChaikuad, A. / Akutsu, M. / Lotz, R. / Osterburg, C. / Knapp, S. / Dotsch, V.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)DO 545/18-1 Germany
German Research Foundation (DFG)DO 545/20-1 Germany
CitationJournal: Cell Death Dis / Year: 2025
Title: Alternative splicing in the DBD linker region of p63 modulates binding to DNA and iASPP in vitro.
Authors: Lotz, R. / Osterburg, C. / Chaikuad, A. / Weber, S. / Akutsu, M. / Machel, A.C. / Beyer, U. / Gebel, J. / Lohr, F. / Knapp, S. / Dobbelstein, M. / Lu, X. / Dotsch, V.
History
DepositionAug 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Tumor protein 63,RelA-associated inhibitor
BBB: Tumor protein 63,RelA-associated inhibitor
CCC: Tumor protein 63,RelA-associated inhibitor
DDD: Tumor protein 63,RelA-associated inhibitor


Theoretical massNumber of molelcules
Total (without water)92,1704
Polymers92,1704
Non-polymers00
Water1,31573
1
AAA: Tumor protein 63,RelA-associated inhibitor


Theoretical massNumber of molelcules
Total (without water)23,0431
Polymers23,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Tumor protein 63,RelA-associated inhibitor


Theoretical massNumber of molelcules
Total (without water)23,0431
Polymers23,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Tumor protein 63,RelA-associated inhibitor


Theoretical massNumber of molelcules
Total (without water)23,0431
Polymers23,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Tumor protein 63,RelA-associated inhibitor


Theoretical massNumber of molelcules
Total (without water)23,0431
Polymers23,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.119, 94.120, 179.314
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA BBB
22Chains AAA CCC
33Chains AAA DDD
44Chains BBB CCC
55Chains BBB DDD
66Chains CCC DDD

NCS ensembles :
ID
1
6
2
3
4
5

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Components

#1: Protein
Tumor protein 63,RelA-associated inhibitor / p63 / Chronic ulcerative stomatitis protein / CUSP / Keratinocyte transcription factor KET / ...p63 / Chronic ulcerative stomatitis protein / CUSP / Keratinocyte transcription factor KET / Transformation-related protein 63 / TP63 / Tumor protein p73-like / p73L / p40 / p51 / Inhibitor of ASPP protein / Protein iASPP / NFkB-interacting protein 1 / PPP1R13B-like protein


Mass: 23042.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: TP63, KET, P63, P73H, P73L, TP73L, PPP1R13L, IASPP, NKIP1, PPP1R13BL, RAI
Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3D4, UniProt: Q8WUF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2 M sodium formate and 0.1 M TRIS pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→47.244 Å / Num. obs: 51860 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.4
Reflection shellResolution: 2.4→2.47 Å / Rmerge(I) obs: 0.2135 / Num. unique obs: 4431 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.244 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.643 / SU ML: 0.248 / Cross valid method: FREE R-VALUE / ESU R: 0.311 / ESU R Free: 0.247
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2796 2550 4.919 %
Rwork0.2428 49286 -
all0.245 --
obs-51860 99.904 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 69.485 Å2
Baniso -1Baniso -2Baniso -3
1--0.435 Å20 Å20 Å2
2--2.755 Å2-0 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6383 0 0 73 6456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136544
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175689
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.6368931
X-RAY DIFFRACTIONr_angle_other_deg1.1631.56813207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.745826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69723.428353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65115957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1911532
X-RAY DIFFRACTIONr_chiral_restr0.0440.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027555
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021393
X-RAY DIFFRACTIONr_nbd_refined0.2130.21163
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.24990
X-RAY DIFFRACTIONr_nbtor_refined0.1620.23202
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.274
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.241
X-RAY DIFFRACTIONr_nbd_other0.2610.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3460.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.150.23
X-RAY DIFFRACTIONr_mcbond_it6.4087.2613316
X-RAY DIFFRACTIONr_mcbond_other6.4067.263315
X-RAY DIFFRACTIONr_mcangle_it9.57710.8884138
X-RAY DIFFRACTIONr_mcangle_other9.57510.894139
X-RAY DIFFRACTIONr_scbond_it6.3177.8233228
X-RAY DIFFRACTIONr_scbond_other6.3177.8243229
X-RAY DIFFRACTIONr_scangle_it9.63611.4724793
X-RAY DIFFRACTIONr_scangle_other9.63611.4724793
X-RAY DIFFRACTIONr_lrange_it13.11283.0876994
X-RAY DIFFRACTIONr_lrange_other13.11183.1016995
X-RAY DIFFRACTIONr_ncsr_local_group_10.0530.056403
X-RAY DIFFRACTIONr_ncsr_local_group_20.0610.056275
X-RAY DIFFRACTIONr_ncsr_local_group_30.0540.056374
X-RAY DIFFRACTIONr_ncsr_local_group_40.0720.056236
X-RAY DIFFRACTIONr_ncsr_local_group_50.060.056341
X-RAY DIFFRACTIONr_ncsr_local_group_60.0620.056293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.3951850.3843570X-RAY DIFFRACTION99.9468
2.462-2.5290.3981570.3863512X-RAY DIFFRACTION99.9183
2.529-2.6030.3581790.3463412X-RAY DIFFRACTION99.9722
2.603-2.6820.391750.3273300X-RAY DIFFRACTION99.9712
2.682-2.770.3411570.3263242X-RAY DIFFRACTION99.9412
2.77-2.8670.3471580.3233084X-RAY DIFFRACTION99.8768
2.867-2.9750.3691470.3263004X-RAY DIFFRACTION100
2.975-3.0960.3171540.2952896X-RAY DIFFRACTION100
3.096-3.2330.3341410.2922786X-RAY DIFFRACTION99.9317
3.233-3.390.3521510.2872667X-RAY DIFFRACTION100
3.39-3.5720.2661180.262544X-RAY DIFFRACTION100
3.572-3.7870.2921250.2392402X-RAY DIFFRACTION99.9209
3.787-4.0470.2681230.2212294X-RAY DIFFRACTION100
4.047-4.3690.261000.1982101X-RAY DIFFRACTION99.5027
4.369-4.7820.2161220.1831954X-RAY DIFFRACTION99.9519
4.782-5.3390.262950.181783X-RAY DIFFRACTION99.8936
5.339-6.1520.228930.2021593X-RAY DIFFRACTION100
6.152-7.5030.221670.1991382X-RAY DIFFRACTION99.8622

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