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- PDB-8p9c: Crystal structure of p63-p73 heterotetramer (tetramerisation doma... -

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Basic information

Entry
Database: PDB / ID: 8p9c
TitleCrystal structure of p63-p73 heterotetramer (tetramerisation domain) in complex with darpin 1810 F11
Components
  • Darpin 1810 F11
  • Tumor protein 63
  • Tumor protein p73
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 / negative regulation of mesoderm development / prostatic bud formation / female genitalia morphogenesis / positive regulation of keratinocyte proliferation / establishment of planar polarity ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / positive regulation of lung ciliated cell differentiation / 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 / negative regulation of cardiac muscle cell proliferation / 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 / positive regulation of oligodendrocyte differentiation / negative regulation of cellular senescence / keratinocyte proliferation / negative regulation of neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Pyroptosis / establishment of skin barrier / positive regulation of osteoblast differentiation / mismatch repair / keratinocyte differentiation / Notch signaling pathway / MDM2/MDM4 family protein binding / regulation of mitotic cell cycle / positive regulation of apoptotic signaling pathway / transcription corepressor binding / stem cell proliferation / kidney development / 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 / 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 / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / spermatogenesis / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / damaged DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / positive regulation of MAPK cascade / regulation of cell cycle / ciliary basal body / positive regulation of apoptotic process / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / apoptotic process / centrosome / dendrite / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex
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: 1.76 Å
AuthorsChaikuad, A. / Strubel, A. / Doetsch, V. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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.
History
DepositionJun 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_assembly
Item: _entity.src_method / _pdbx_struct_assembly.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,5367
Polymers30,2883
Non-polymers2484
Water2,954164
1
A: Tumor protein 63
B: Tumor protein p73
C: Darpin 1810 F11
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)61,07314
Polymers60,5766
Non-polymers4978
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area16300 Å2
ΔGint-99 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.024, 60.312, 53.576
Angle α, β, γ (deg.)90.00, 100.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 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: 7380.242 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 / p53-like transcription factor / p53-related protein


Mass: 6034.894 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium acetate, 25% PEG3350, 0.1M HEPES 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 EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→48.73 Å / Num. obs: 25297 / % possible obs: 96.7 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.031 / Rrim(I) all: 0.063 / Χ2: 0.71 / Net I/σ(I): 12.2
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2481 / CC1/2: 0.899 / Rpim(I) all: 0.241 / Rrim(I) all: 0.484 / Χ2: 0.36

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→48.73 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.183 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21012 1197 4.7 %RANDOM
Rwork0.16991 ---
obs0.17184 24099 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.202 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0 Å2-0.11 Å2
2--0.96 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.76→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 16 164 2227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132135
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171997
X-RAY DIFFRACTIONr_angle_refined_deg1.471.6352890
X-RAY DIFFRACTIONr_angle_other_deg1.4321.5764661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4835268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4625.431116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46215394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.37157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022383
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02374
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_it1.882.1041048
X-RAY DIFFRACTIONr_mcbond_other1.8742.1031047
X-RAY DIFFRACTIONr_mcangle_it2.9463.1351309
X-RAY DIFFRACTIONr_mcangle_other2.9473.1371310
X-RAY DIFFRACTIONr_scbond_it2.7842.5611087
X-RAY DIFFRACTIONr_scbond_other2.7822.5631088
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3743.6741577
X-RAY DIFFRACTIONr_long_range_B_refined6.69826.3752484
X-RAY DIFFRACTIONr_long_range_B_other6.69626.392485
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 84 -
Rwork0.234 1759 -
obs--96.8 %
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)
10.9746-0.08011.01740.10550.07511.7294-0.108-0.09920.103-0.0394-0.02730.0028-0.0768-0.07430.13540.06680.0368-0.01520.16510.00220.014132.0452.61420.933
20.3219-0.68540.70071.8657-1.66591.72580.01390.07230.05290.0043-0.1752-0.0248-0.00340.11940.16120.0061-0.0018-0.0050.18470.01150.090234.0562.45919.857
30.8362-0.2654-0.18370.8461-0.52112.1679-0.02190.025-0.0091-0.0883-0.01980.08360.13350.14350.04170.04330.0386-0.01070.1194-0.00520.016119.13812.6613.329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A359 - 412
2X-RAY DIFFRACTION2B352 - 396
3X-RAY DIFFRACTION3C1 - 159

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