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- PDB-3us0: Structure of p63 DNA Binding Domain in Complex with a 22 Base Pai... -

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Basic information

Entry
Database: PDB / ID: 3us0
TitleStructure of p63 DNA Binding Domain in Complex with a 22 Base Pair A/T Rich Response Element Containing a Two Base Pair "AT" Spacer Between Half Sites
Components
  • 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
  • Tumor protein 63
KeywordsTRANSCRIPTION ACTIVATOR/DNA / B-DNA double helix / zinc binding / beta sandwich / Greek key / transcription factor / nucleus / TRANSCRIPTION ACTIVATOR-DNA complex
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 / Immunoglobulin-like - #720 / 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 / Immunoglobulin-like - #720 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Tumor protein 63
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, C. / Herzberg, O.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Pliable DNA Conformation of Response Elements Bound to Transcription Factor p63.
Authors: Chen, C. / Gorlatova, N. / Herzberg, O.
History
DepositionNov 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor protein 63
B: Tumor protein 63
C: Tumor protein 63
D: Tumor protein 63
E: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
F: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,49410
Polymers104,2326
Non-polymers2624
Water7,098394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.806, 141.806, 119.604
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Tumor protein 63 / TP63 / p63 / Chronic ulcerative stomatitis protein / CUSP / Keratinocyte transcription factor KET / ...TP63 / p63 / Chronic ulcerative stomatitis protein / CUSP / Keratinocyte transcription factor KET / Transformation-related protein 63 / Tumor protein p73-like / p73L / p40 / p51


Mass: 22683.861 Da / Num. of mol.: 4 / Fragment: DNA binding domain (UNP residues 166-362)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KET, P63, P73H, P73L, TP63, TP73L / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9H3D4
#2: DNA chain 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'


Mass: 6748.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: P63 response element with AT Spacer
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 394 / 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: 3.33 Å3/Da / Density % sol: 63.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 14% PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03320357 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2010 / Details: mirrors
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03320357 Å / Relative weight: 1
ReflectionResolution: 2.5→60 Å / Num. all: 47269 / Num. obs: 47258 / % possible obs: 99.99 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 3.5 / Redundancy: 12.8 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.9
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3446 / % possible all: 100

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QYN

3qyn


Resolution: 2.5→59.802 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 28.66 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 2424 5.13 %RANDOM
Rwork0.206 ---
obs0.2077 47224 99.91 %-
all-47269 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.183 Å2 / ksol: 0.283 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.4619 Å2-0 Å2-0 Å2
2--8.4619 Å20 Å2
3----16.9237 Å2
Refinement stepCycle: LAST / Resolution: 2.5→59.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5985 896 4 394 7279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117136
X-RAY DIFFRACTIONf_angle_d1.6439894
X-RAY DIFFRACTIONf_dihedral_angle_d20.3442741
X-RAY DIFFRACTIONf_chiral_restr0.1021105
X-RAY DIFFRACTIONf_plane_restr0.0071151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5510.4091520.38412593X-RAY DIFFRACTION100
2.551-2.60650.38651320.35852648X-RAY DIFFRACTION100
2.6065-2.66710.38331440.35642603X-RAY DIFFRACTION100
2.6671-2.73380.40281550.3432647X-RAY DIFFRACTION100
2.7338-2.80780.35691360.32972614X-RAY DIFFRACTION100
2.8078-2.89040.28261450.30442629X-RAY DIFFRACTION100
2.8904-2.98370.32861440.28562631X-RAY DIFFRACTION100
2.9837-3.09030.29581550.25772623X-RAY DIFFRACTION100
3.0903-3.2140.2481400.22862609X-RAY DIFFRACTION100
3.214-3.36030.21881140.18622654X-RAY DIFFRACTION100
3.3603-3.53740.27821440.21862634X-RAY DIFFRACTION100
3.5374-3.7590.21441430.20022627X-RAY DIFFRACTION100
3.759-4.04920.21161320.18792659X-RAY DIFFRACTION100
4.0492-4.45660.17481370.15252633X-RAY DIFFRACTION100
4.4566-5.10120.17121470.13892646X-RAY DIFFRACTION100
5.1012-6.42570.18521580.14972650X-RAY DIFFRACTION100
6.4257-59.81910.21781460.17052700X-RAY DIFFRACTION100
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)
11.3233-0.7895-0.48571.96181.21661.03460.12440.16730.0185-0.461-0.25540.1854-0.4676-0.2446-0.00960.47950.0834-0.08290.3339-0.01120.3942-59.50236.393622.697
20.9242-0.3418-0.11411.32740.50511.79920.07820.1531-0.0466-0.2589-0.24350.0165-0.21-0.085800.38670.0565-0.02160.359-0.00580.3896-49.0776-19.9373-10.3005
31.21890.79790.25270.52660.28180.43260.3692-0.57540.11460.4752-0.33670.37380.1902-0.36640.07150.5143-0.17720.11440.6061-0.07370.5374-57.327520.3927-43.4989
41.08130.40560.11261.28840.60551.19550.2012-0.38910.00310.4466-0.3031-0.00320.2986-0.2738-0.00110.5069-0.13310.04360.4718-0.01610.3283-36.254339.5497-10.1073
5-0.31250.4698-0.84581.3089-2.95061.46120.08550.0026-0.0516-0.1963-0.0042-0.02750.23370.61540.05030.8691-0.14120.0320.52630.08150.3928-36.4128.2543-10.1442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E or chain F

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