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- PDB-7z71: Crystal structure of p63 DBD in complex with darpin C14 -

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Basic information

Entry
Database: PDB / ID: 7z71
TitleCrystal structure of p63 DBD in complex with darpin C14
Components
  • Darpin C14
  • Isoform 4 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 / 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 ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / 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 / positive regulation of cell cycle G1/S phase transition / proximal/distal pattern formation / positive regulation of fibroblast apoptotic process / 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 Notch signaling pathway / regulation of epidermal cell division / positive regulation of stem cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / epithelial cell development / TP53 Regulates Transcription of Caspase Activators and Caspases / odontogenesis of dentin-containing tooth / negative regulation of cellular senescence / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / keratinocyte proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / MDM2/MDM4 family protein binding / positive regulation of osteoblast differentiation / establishment of skin barrier / Pyroptosis / positive regulation of apoptotic signaling pathway / keratinocyte differentiation / Notch signaling pathway / skeletal system development / stem cell proliferation / determination of adult lifespan / TP53 Regulates Metabolic Genes / protein tetramerization / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular senescence / p53 binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / 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 / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / metal ion 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: 1.85 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 4 of Tumor protein 63
B: Darpin C14
C: Isoform 4 of Tumor protein 63
D: Darpin C14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9026
Polymers78,7714
Non-polymers1312
Water12,394688
1
A: Isoform 4 of Tumor protein 63
B: Darpin C14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4513
Polymers39,3862
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-0 kcal/mol
Surface area16160 Å2
MethodPISA
2
C: Isoform 4 of Tumor protein 63
D: Darpin C14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4513
Polymers39,3862
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-5 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.033, 63.930, 65.504
Angle α, β, γ (deg.)114.460, 94.600, 104.060
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAILEILEAA125 - 3205 - 200
21ALAALAILEILECC125 - 3205 - 200
12ASPASPALAALABB3 - 1593 - 159
22ASPASPALAALADD3 - 1593 - 159

NCS ensembles :
ID
1
2

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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.: 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 Darpin C14


Mass: 16632.615 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.2 M sodium chloride, 0.1 M 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: 1.00003 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.85→44.64 Å / Num. obs: 58153 / % possible obs: 91.6 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.025 / Rrim(I) all: 0.048 / Net I/σ(I): 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.913.80.119.557680.9750.0840.16192.6
7.17-44.643.60.0249950.9990.0150.02891

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qyn, 6fpb

3qyn

6fpb


Resolution: 1.85→42.69 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.005 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 2857 4.9 %RANDOM
Rwork0.142 ---
obs0.1439 55294 91.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.01 Å2 / Biso mean: 27.074 Å2 / Biso min: 14.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20.06 Å2-0.2 Å2
2--0.07 Å21.15 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 1.85→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5334 0 2 688 6024
Biso mean--23.93 35.15 -
Num. residues----699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0135504
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175234
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.6437503
X-RAY DIFFRACTIONr_angle_other_deg1.4531.57912104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0445716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7523.456272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52715919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8041529
X-RAY DIFFRACTIONr_chiral_restr0.0890.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026318
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021156
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A56520.12
12C56520.12
21B48360.08
22D48360.08
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 206 -
Rwork0.147 4159 -
all-4365 -
obs--92.36 %
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)
10.359-0.18580.11340.5202-0.22580.57110.0360.00950.0324-0.0308-0.0232-0.0004-0.0011-0.0448-0.01280.0461-0.0057-0.03380.05410.02560.055722.550925.200936.4866
20.257-0.33710.28950.9456-0.15091.57030.01760.01750.03-0.0117-0.0473-0.1008-0.039800.02970.0258-0.0079-0.03350.03510.02980.067629.411228.41238.844
30.433-0.16990.55040.2402-0.16020.73040.10330.0164-0.0258-0.0843-0.05070.03980.1347-0.0116-0.05270.0504-0.0051-0.04110.06760.03110.061119.098424.316332.2493
43.42891.4426-0.78551.07450.65072.29130.03210.0257-0.27890.01230.0575-0.22-0.04860.1332-0.08960.0282-0.0257-0.0410.03920.03530.138834.073445.224914.7828
50.94370.0576-0.19060.58970.04410.35620.0008-0.0556-0.0039-0.01310.007-0.0365-0.0517-0.0455-0.00780.0275-0.0023-0.03020.04280.03730.070212.881441.815715.9965
65.5074-4.03842.29986.5799-2.26154.3842-0.0085-0.19420.10560.3867-0.0250.1793-0.1498-0.21780.03350.045-0.00020.02870.12650.0380.0641-2.587841.060427.0247
70.3988-0.3380.04271.3952-0.39050.55730.031-0.0280.0291-0.0147-0.0549-0.03830.00970.01680.02390.0284-0.0065-0.030.01530.01420.061312.93543.1613.4715
80.43110.16570.08080.7951-0.31020.2590.0373-0.01070.0297-0.0014-0.01580.01540.0357-0.0218-0.02150.0457-0.0029-0.03140.02850.01740.07558.66061.0522.4679
90.04540.14750.01012.6545-1.0050.52270.020.00310.02040.0424-0.06880.0416-0.00760.06350.04880.033-0.0055-0.01740.03190.0210.116319.29296.7813.8989
104.49760.354-0.21461.04350.10792.55720.0289-0.08070.12360.0049-0.05810.21840.2859-0.33480.02920.0431-0.0417-0.03260.05070.00010.1684-0.775727.0726-4.1448
111.05030.2696-0.17360.6008-0.08180.4148-0.04530.0419-0.0492-0.0721-0.00770.0561-0.01840.02040.0530.0345-0.0161-0.04590.0160.0160.091816.36930.1754-6.1655
121.9093-0.0629-0.22762.04280.31833.147-0.08810.0864-0.1429-0.2534-0.0746-0.26210.00080.49120.16270.04080.00720.02530.09360.04450.12133.965627.6979-10.7929
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 211
2X-RAY DIFFRACTION2A212 - 290
3X-RAY DIFFRACTION3A291 - 320
4X-RAY DIFFRACTION4B3 - 26
5X-RAY DIFFRACTION5B27 - 144
6X-RAY DIFFRACTION6B145 - 159
7X-RAY DIFFRACTION7C125 - 219
8X-RAY DIFFRACTION8C220 - 290
9X-RAY DIFFRACTION9C291 - 320
10X-RAY DIFFRACTION10D3 - 26
11X-RAY DIFFRACTION11D27 - 116
12X-RAY DIFFRACTION12D117 - 159

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