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- PDB-7z7e: Crystal structure of p63 DNA binding domain in complex with inhib... -

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Basic information

Entry
Database: PDB / ID: 7z7e
TitleCrystal structure of p63 DNA binding domain in complex with inhibitory DARPin G4
Components
  • DARPIN
  • Isoform 4 of Tumor protein 63
KeywordsTRANSCRIPTION / p63 DBD / DARPin / Inhibitor
Function / homology
Function and homology information


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 / positive regulation of keratinocyte proliferation / establishment of planar polarity / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development ...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 / 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 / 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 / keratinocyte differentiation / Notch signaling pathway / MDM2/MDM4 family protein binding / positive regulation of apoptotic signaling pathway / stem cell proliferation / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / determination of adult lifespan / TP53 Regulates Metabolic Genes / protein tetramerization / promoter-specific chromatin binding / cellular senescence / p53 binding / 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 / 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 / cytoplasm
Similarity search - Function
Tumour protein p63, SAM 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) ...Tumour protein p63, SAM 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStrubel, A. / Gebel, J. / Chaikuad, A. / Muenick, P. / Doetsch, V.
Funding support Germany, Canada, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)DO 545/13-1 Germany
German Research Foundation (DFG)DO 545/18-1 Germany
The Structural Genomics Consortium (SGC)1097737 Canada
CitationJournal: Cell Death Differ. / Year: 2022
Title: Designed Ankyrin Repeat Proteins as a tool box for analyzing p63.
Authors: Strubel, A. / Munick, P. / Chaikuad, A. / Dreier, B. / Schaefer, J. / Gebel, J. / Osterburg, C. / Tuppi, M. / Schafer, B. / Knapp, S. / Pluckthun, A. / Dotsch, V.
History
DepositionMar 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 4 of Tumor protein 63
B: DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7273
Polymers39,6622
Non-polymers651
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Purified proteins co-migrate on size exclusion chromatography, hence forming a stable complex., immunoprecipitation, DARPin immunoprecipitates full length p63 protein from ...Evidence: gel filtration, Purified proteins co-migrate on size exclusion chromatography, hence forming a stable complex., immunoprecipitation, DARPin immunoprecipitates full length p63 protein from cell lysate of human cells.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-14 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.578, 96.578, 77.071
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Isoform 4 of Tumor protein 63 / 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


Mass: 22752.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP63, KET, P63, P73H, P73L, TP73L / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9H3D4
#2: Protein DARPIN


Mass: 16908.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 25% PEG 3350 0.2M Li2SO4 0.1M HEPES / PH range: 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 EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.29 Å / Num. obs: 37301 / % possible obs: 96.4 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.012 / Rpim(I) all: 0.019 / Rrim(I) all: 0.027 / Net I/σ(I): 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-48.291.70.0153580.9990.0150.022
1.8-1.841.90.31622110.8260.3160.447

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHASERphasing
BUCCANEERmodel building
Cootmodel building
Aimlessdata scaling
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3US0

3us0


Resolution: 1.8→48.29 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.33 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2488 1865 5 %
Rwork0.1967 35434 -
all0.199 --
obs-37299 95.99 %
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: 40.609 Å2
Baniso -1Baniso -2Baniso -3
1-0.398 Å20.199 Å20 Å2
2--0.398 Å2-0 Å2
3----1.293 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 1 186 2866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132736
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152569
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.6433721
X-RAY DIFFRACTIONr_angle_other_deg1.3561.5785929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.255348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.80122.941136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48415441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8891515
X-RAY DIFFRACTIONr_chiral_restr0.080.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02580
X-RAY DIFFRACTIONr_nbd_refined0.2050.2535
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.22424
X-RAY DIFFRACTIONr_nbtor_refined0.160.21318
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21265
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2147
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.26
X-RAY DIFFRACTIONr_nbd_other0.210.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.24
X-RAY DIFFRACTIONr_mcbond_it3.7154.1441401
X-RAY DIFFRACTIONr_mcbond_other3.7134.1421400
X-RAY DIFFRACTIONr_mcangle_it4.8946.1891746
X-RAY DIFFRACTIONr_mcangle_other4.8926.1911747
X-RAY DIFFRACTIONr_scbond_it4.1394.5241335
X-RAY DIFFRACTIONr_scbond_other4.1384.5261336
X-RAY DIFFRACTIONr_scangle_it5.9546.6321975
X-RAY DIFFRACTIONr_scangle_other5.9526.6341976
X-RAY DIFFRACTIONr_lrange_it7.48849.572963
X-RAY DIFFRACTIONr_lrange_other7.49249.4672938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3151370.3142611X-RAY DIFFRACTION96.3534
1.847-1.8970.341340.2882552X-RAY DIFFRACTION96.6883
1.897-1.9520.3281280.2672431X-RAY DIFFRACTION96.2754
1.952-2.0120.2761180.2642243X-RAY DIFFRACTION89.5336
2.012-2.0780.2851200.2532269X-RAY DIFFRACTION95.1414
2.078-2.1510.3041210.232300X-RAY DIFFRACTION97.5816
2.151-2.2320.2441150.2112185X-RAY DIFFRACTION97.5403
2.232-2.3230.2951130.2092143X-RAY DIFFRACTION97.5357
2.323-2.4270.2891080.2072054X-RAY DIFFRACTION97.9167
2.427-2.5450.2681020.2071936X-RAY DIFFRACTION98.0279
2.545-2.6830.276970.2131854X-RAY DIFFRACTION96.92
2.683-2.8450.285870.2181640X-RAY DIFFRACTION91.0385
2.845-3.0410.281840.2231597X-RAY DIFFRACTION94.2793
3.041-3.2850.231820.2081561X-RAY DIFFRACTION98.4422
3.285-3.5980.239760.2051453X-RAY DIFFRACTION98.8365
3.598-4.0210.23690.1611311X-RAY DIFFRACTION98.5011
4.021-4.6420.178610.1521151X-RAY DIFFRACTION96.5737
4.642-5.680.214460.161885X-RAY DIFFRACTION87.0907
5.68-8.0150.289420.181790X-RAY DIFFRACTION99.4026
8.015-48.290.199250.153468X-RAY DIFFRACTION98.7976

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