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- PDB-8p9e: Crystal structure of wild type p63-p73 heterotetramer (tetrameris... -

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Basic information

Entry
Database: PDB / ID: 8p9e
TitleCrystal structure of wild type p63-p73 heterotetramer (tetramerisation domain) in complex with darpin 1810 F11
Components
  • Darpin 1810 F11
  • Isoform 2 of Tumor protein 63
  • Tumor protein p73P73
KeywordsDNA BINDING PROTEIN / p63 / p73 / tetramerization domain / darpin / heterotetramer / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / positive regulation of lung ciliated cell differentiation / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / establishment of planar polarity / positive regulation of keratinocyte proliferation ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / positive regulation of lung ciliated cell differentiation / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / establishment of planar polarity / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / polarized epithelial cell differentiation / negative regulation of intracellular estrogen receptor signaling pathway / proximal/distal pattern formation / negative regulation of cardiac muscle cell proliferation / positive regulation of fibroblast apoptotic process / positive regulation of cell cycle G1/S phase transition / WW domain binding / skin morphogenesis / cranial skeletal system development / sympathetic nervous system development / post-anal tail morphogenesis / embryonic forelimb morphogenesis / 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 / positive regulation of oligodendrocyte differentiation / positive regulation of Notch signaling pathway / regulation of epidermal cell division / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of stem cell proliferation / TP53 Regulates Transcription of Caspase Activators and Caspases / epithelial cell development / odontogenesis of dentin-containing tooth / negative regulation of cellular senescence / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / keratinocyte proliferation / negative regulation of neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / establishment of skin barrier / mismatch repair / Pyroptosis / positive regulation of osteoblast differentiation / keratinocyte differentiation / MDM2/MDM4 family protein binding / Notch signaling pathway / response to organonitrogen compound / regulation of mitotic cell cycle / transcription corepressor binding / kidney development / skeletal system development / stem cell proliferation / positive regulation of apoptotic signaling pathway / determination of adult lifespan / promoter-specific chromatin binding / TP53 Regulates Metabolic Genes / protein tetramerization / RNA polymerase II transcription regulatory region sequence-specific DNA binding / intrinsic apoptotic signaling pathway in response to DNA damage / cellular senescence / p53 binding / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / spermatogenesis / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / positive regulation of MAPK cascade / damaged DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / chromatin remodeling / response to xenobiotic stimulus / positive regulation of apoptotic process / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / dendrite / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm
Similarity search - Function
Tumour protein p63, SAM domain / Tumour protein p73, 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 ...Tumour protein p63, SAM domain / Tumour protein p73, 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
Tumor protein p73 / Tumor protein 63
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsChaikuad, A. / Strubel, A. / Doetsch, V. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Cell Death Dis / Year: 2023
Title: DARPins detect the formation of hetero-tetramers of p63 and p73 in epithelial tissues and in squamous cell carcinoma.
Authors: Strubel, A. / Munick, P. / Hartmann, O. / Chaikuad, A. / Dreier, B. / Schaefer, J.V. / Gebel, J. / Osterburg, C. / Tuppi, M. / Schafer, B. / Buck, V. / Rosenfeldt, M. / Knapp, S. / ...Authors: Strubel, A. / Munick, P. / Hartmann, O. / Chaikuad, A. / Dreier, B. / Schaefer, J.V. / Gebel, J. / Osterburg, C. / Tuppi, M. / Schafer, B. / Buck, V. / Rosenfeldt, M. / Knapp, S. / Pluckthun, A. / Diefenbacher, M.E. / Dotsch, V.
#1: Journal: Chemmedchem / Year: 2023
Title: Structural Basis of Saccharin Derivative Inhibition of Carbonic Anhydrase IX.
Authors: Leitans, J. / Kazaks, A. / Bogans, J. / Supuran, C.T. / Akopjana, I. / Ivanova, J. / Zalubovskis, R. / Tars, K.
History
DepositionJun 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_entity_src_syn
Item: _citation.journal_id_ISSN / _entity.pdbx_description / _entity.src_method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Tumor protein 63
B: Tumor protein p73
C: Darpin 1810 F11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3804
Polymers30,2883
Non-polymers921
Water52229
1
A: Isoform 2 of Tumor protein 63
B: Tumor protein p73
C: Darpin 1810 F11
hetero molecules

A: Isoform 2 of Tumor protein 63
B: Tumor protein p73
C: Darpin 1810 F11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7608
Polymers60,5766
Non-polymers1842
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)84.704, 60.728, 53.866
Angle α, β, γ (deg.)90.00, 100.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Isoform 2 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: 7380.309 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 (E. coli) / References: UniProt: Q9H3D4
#2: Protein/peptide Tumor protein p73 / P73 / p53-like transcription factor / p53-related protein


Mass: 6034.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP73, P73 / Production host: Escherichia coli (E. coli) / References: UniProt: O15350
#3: Protein Darpin 1810 F11


Mass: 16872.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M sodium chloride, 25% PEG3350, 0.1M bis-tris pH 6.5

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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: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→49.05 Å / Num. obs: 12746 / % possible obs: 99.4 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.042 / Rrim(I) all: 0.113 / Χ2: 0.87 / Net I/σ(I): 8.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1208 / CC1/2: 0.883 / Rpim(I) all: 0.344 / Rrim(I) all: 0.905 / Χ2: 0.86

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→49.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.926 / SU B: 20.913 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25012 643 5 %RANDOM
Rwork0.18932 ---
obs0.19226 12100 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.647 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20.86 Å2
2--6.78 Å20 Å2
3----6.59 Å2
Refinement stepCycle: 1 / Resolution: 2.25→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 6 29 2103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132103
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171956
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.632845
X-RAY DIFFRACTIONr_angle_other_deg1.2431.5764559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9865259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85825.398113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35515384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.754157
X-RAY DIFFRACTIONr_chiral_restr0.0610.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022341
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02368
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4143.8951045
X-RAY DIFFRACTIONr_mcbond_other2.4153.8931044
X-RAY DIFFRACTIONr_mcangle_it3.8075.8181301
X-RAY DIFFRACTIONr_mcangle_other3.8065.8211302
X-RAY DIFFRACTIONr_scbond_it3.2574.3981058
X-RAY DIFFRACTIONr_scbond_other3.2554.4021059
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2966.4021545
X-RAY DIFFRACTIONr_long_range_B_refined7.20146.2482293
X-RAY DIFFRACTIONr_long_range_B_other7.19946.2682293
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 47 -
Rwork0.313 849 -
obs--98.57 %
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)
12.33470.1071.60320.8578-0.61382.557-0.1647-0.04130.3493-0.0083-0.05780.204-0.22010.030.22250.02710.02-0.05260.2491-0.0030.25632.18472.716721.0936
20.2583-0.17020.28832.5698-1.9642.31070.05830.05280.0816-0.0293-0.22730.00970.03770.15150.1690.0338-0.0076-0.05970.24930.03160.313334.25212.617719.5975
31.9867-0.1735-0.74840.5555-0.46153.1327-0.02990.0478-0.0441-0.0917-0.09650.10380.07140.12480.12640.06050.0606-0.06750.1351-0.01120.255619.204312.69533.4388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A357 - 413
2X-RAY DIFFRACTION2B352 - 397
3X-RAY DIFFRACTION3C1 - 159

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