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- PDB-7z73: Crystal structure of p63 tetramerization domain in complex with d... -

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Basic information

Entry
Database: PDB / ID: 7z73
TitleCrystal structure of p63 tetramerization domain in complex with darpin 8F1
Components
  • Darpin 8F1
  • Isoform 2 of Tumor protein 63
KeywordsDNA BINDING PROTEIN / p63 / TP63 / darpin / 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 / 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 / proximal/distal pattern formation / positive regulation of fibroblast apoptotic process / skin morphogenesis / positive regulation of cell cycle G1/S phase transition / negative regulation of intracellular estrogen receptor signaling pathway / sympathetic nervous system development / cranial skeletal 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 / epithelial cell development / TP53 Regulates Transcription of Caspase Activators and Caspases / positive regulation of Notch signaling pathway / regulation of epidermal cell division / positive regulation of stem cell proliferation / 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 / determination of adult lifespan / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein tetramerization / promoter-specific chromatin binding / p53 binding / cellular senescence / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / spermatogenesis / damaged DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / dendrite / 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: 2.27 Å
AuthorsChaikuad, A. / Strubel, A. / Doetsch, V. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
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 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Tumor protein 63
B: Isoform 2 of Tumor protein 63
C: Isoform 2 of Tumor protein 63
D: Isoform 2 of Tumor protein 63
E: Darpin 8F1
F: Darpin 8F1


Theoretical massNumber of molelcules
Total (without water)56,6526
Polymers56,6526
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
ΔGint-88 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.563, 50.761, 65.858
Angle α, β, γ (deg.)80.930, 79.920, 68.750
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLNGLNAA360 - 4055 - 50
21GLUGLUGLNGLNBB360 - 4055 - 50
12ASPASPGLNGLNAA359 - 4014 - 46
22ASPASPGLNGLNCC359 - 4014 - 46
13GLUGLUGLNGLNAA360 - 4015 - 46
23GLUGLUGLNGLNDD360 - 4015 - 46
14GLUGLUGLNGLNBB360 - 4015 - 46
24GLUGLUGLNGLNCC360 - 4015 - 46
15GLUGLUGLNGLNBB360 - 4015 - 46
25GLUGLUGLNGLNDD360 - 4015 - 46
16GLUGLUGLNGLNCC360 - 4015 - 46
26GLUGLUGLNGLNDD360 - 4015 - 46
17SERSERALAALAEE2 - 1252 - 125
27SERSERALAALAFF2 - 1252 - 125

NCS ensembles :
ID
1
2
3
4
5
6
7

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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.: 4
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 Darpin 8F1


Mass: 13565.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.2 M sodium chloride, 0.1 M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.27→47.06 Å / Num. obs: 21523 / % possible obs: 92.6 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.038 / Rrim(I) all: 0.076 / Net I/σ(I): 11.3 / Num. measured all: 82692 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.27-2.353.90.542811220910.90.3180.6282.291.5
8.79-47.063.80.03215113970.9950.0190.0383098.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zuv, 4a9z

3zuv

4a9z


Resolution: 2.27→47.06 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2431 / WRfactor Rwork: 0.1953 / FOM work R set: 0.8036 / SU B: 15.867 / SU ML: 0.178 / SU R Cruickshank DPI: 0.3363 / SU Rfree: 0.2323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 1065 4.9 %RANDOM
Rwork0.1872 ---
obs0.1896 20456 92.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.83 Å2 / Biso mean: 63.288 Å2 / Biso min: 33.81 Å2
Baniso -1Baniso -2Baniso -3
1--3.37 Å20.27 Å21.08 Å2
2--3 Å22.06 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 2.27→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 0 51 3559
Biso mean---55.15 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133579
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173418
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.6434847
X-RAY DIFFRACTIONr_angle_other_deg1.2281.5837860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.61323.951205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18415642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7491518
X-RAY DIFFRACTIONr_chiral_restr0.0630.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024075
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02790
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A13560.13
12B13560.13
21A11710.17
22C11710.17
31A11720.16
32D11720.16
41B11470.17
42C11470.17
51B11590.17
52D11590.17
61C11550.15
62D11550.15
71E39020.1
72F39020.1
LS refinement shellResolution: 2.27→2.329 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 65 -
Rwork0.255 1482 -
all-1547 -
obs--90.15 %
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)
15.25211.5835-2.9151.5047-2.18423.4790.00870.0728-0.0671-0.10790.040.13880.13770.1049-0.04880.1061-0.00370.03820.11540.07580.109714.3604-37.7515-53.2549
23.3171-1.9319-1.32154.59451.35330.76470.18530.1381-0.0286-0.247-0.2582-0.0344-0.0555-0.08450.07290.13640.08910.08590.06560.04640.07361.6443-33.165-43.0849
34.0153-2.9726-0.8192.6552.53888.66680.10430.2231-0.39320.1472-0.12120.30460.7578-0.00080.01690.19060.01980.05750.17060.05180.120511.4393-34.3704-55.8577
42.15130.5602-0.5441.9466-1.65982.35380.1941-0.30950.2198-0.0185-0.03570.272-0.10720.0313-0.15840.09690.00590.07240.06370.01030.133-16.948-21.9092-26.4774
52.67610.8233-3.72230.2873-0.98857.5280.0631-0.22770.1256-0.0178-0.10120.04370.08140.47060.0380.1210.0860.03920.09010.01850.02963.94-29.67-42.7908
61.677-0.114-0.26771.9490.5482.0608-0.0539-0.0331-0.05710.01310.03420.03430.04920.18910.01960.03470.03030.040.03790.03210.047432.6145-39.5648-73.5647
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A359 - 406
2X-RAY DIFFRACTION2B360 - 407
3X-RAY DIFFRACTION3C359 - 402
4X-RAY DIFFRACTION4E1 - 126
5X-RAY DIFFRACTION5D360 - 401
6X-RAY DIFFRACTION6F2 - 126

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