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- PDB-8p9d: Crystal structure of p63-p73 heterotetramer (tetramerisation doma... -

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Basic information

Entry
Database: PDB / ID: 8p9d
TitleCrystal structure of p63-p73 heterotetramer (tetramerisation domain) in complex with darpin 1810 A2
Components
  • Darpin 1810 A2
  • Tumor protein 63Neoplasm
  • 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: 2.7 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: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_assembly
Item: _citation.journal_id_ISSN / _entity.pdbx_description ..._citation.journal_id_ISSN / _entity.pdbx_description / _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: Tumor protein 63
D: Tumor protein p73
E: Darpin 1810 A2
F: Darpin 1810 A2


Theoretical massNumber of molelcules
Total (without water)53,2786
Polymers53,2786
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-87 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.729, 113.186, 135.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein Tumor protein 63 / Neoplasm / 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.: 2
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: 6034.894 Da / Num. of mol.: 2
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 A2


Mass: 13223.932 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.1M bis-tris propane pH 7.0, 0.2M salicylic, sodium salt

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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: 2.7→45.08 Å / Num. obs: 17853 / % possible obs: 99.5 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.039 / Rrim(I) all: 0.098 / Χ2: 1.01 / Net I/σ(I): 11.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2 / Num. unique obs: 2555 / CC1/2: 0.751 / Rpim(I) all: 0.393 / Rrim(I) all: 1.01 / Χ2: 1.05

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→43.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 38.382 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R: 0.631 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25164 906 5.1 %RANDOM
Rwork0.21466 ---
obs0.21656 16896 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.644 Å2
Baniso -1Baniso -2Baniso -3
1--4.26 Å2-0 Å20 Å2
2--5.12 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 2.7→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 0 6 3464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133510
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173299
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.6324751
X-RAY DIFFRACTIONr_angle_other_deg1.1191.5787678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8045430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1225.026193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06215640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7931514
X-RAY DIFFRACTIONr_chiral_restr0.0470.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023914
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02629
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_it2.524.8811738
X-RAY DIFFRACTIONr_mcbond_other2.5194.881737
X-RAY DIFFRACTIONr_mcangle_it3.9577.312162
X-RAY DIFFRACTIONr_mcangle_other3.9577.3112163
X-RAY DIFFRACTIONr_scbond_it2.895.2231772
X-RAY DIFFRACTIONr_scbond_other2.8855.2231772
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6377.6952589
X-RAY DIFFRACTIONr_long_range_B_refined6.4357.0643783
X-RAY DIFFRACTIONr_long_range_B_other6.4357.0743784
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A12610.14
12C12610.14
21B12600.13
22D12600.13
31E37790.08
32F37790.08
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 68 -
Rwork0.377 1230 -
obs--100 %
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)
16.51450.99674.63664.6907-0.53368.71740.0784-0.5176-0.36170.2468-0.16510.0662-0.0898-0.19770.08670.29570.06990.10620.22570.01230.11611.196612.4851-0.0911
23.44470.0394-4.19521.5678-1.508211.81150.2687-0.5343-0.46410.271-0.1471-0.1660.23910.4326-0.12160.3765-0.0072-0.1380.37540.02990.333811.11796.3207-0.1099
34.48252.2672-0.67316.0207-3.06148.54320.03040.1087-0.4108-0.7353-0.1454-0.11770.24710.08870.11510.25550.05840.00910.2960.06660.171314.5539.208814.7828
43.03391.53040.66523.43523.60689.6194-0.17880.2186-0.3126-0.45620.10240.24730.3228-0.28760.07640.22670.0427-0.05310.30820.13050.21099.23157.536114.6257
55.7192-3.4982-0.13387.67960.59642.56370.08360.5991-0.0732-0.22650.0804-0.1066-0.27190.1201-0.16410.0347-0.02180.02150.2822-0.06640.023916.742916.5348-23.4808
69.302-1.6713-0.84524.8891-0.5733.74040.1694-0.96140.14240.3017-0.09530.0599-0.1871-0.001-0.07410.0568-0.02030.0030.32860.08230.059617.334812.790238.9618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A359 - 404
2X-RAY DIFFRACTION2B350 - 397
3X-RAY DIFFRACTION3C359 - 404
4X-RAY DIFFRACTION4D352 - 397
5X-RAY DIFFRACTION5E2 - 126
6X-RAY DIFFRACTION6F2 - 126

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