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- PDB-3us2: Structure of p63 DNA Binding Domain in Complex with a 19 Base Pai... -

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Basic information

Entry
Database: PDB / ID: 3us2
TitleStructure of p63 DNA Binding Domain in Complex with a 19 Base Pair A/T Rich Response Element Containing Two Half Sites with a Single Base Pair Overlap
Components
  • 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
  • 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*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 / negative regulation of intracellular estrogen receptor signaling pathway / proximal/distal pattern formation / positive regulation of fibroblast apoptotic process / 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 / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / determination of adult lifespan / TP53 Regulates Metabolic Genes / protein tetramerization / promoter-specific chromatin binding / cellular senescence / p53 binding / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / spermatogenesis / 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 / 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
DNA / DNA (> 10) / Tumor protein 63
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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*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*AP*CP*AP*TP*GP*TP*TP*T)-3'
G: Tumor protein 63
H: Tumor protein 63
I: Tumor protein 63
J: Tumor protein 63
K: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
L: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,28320
Polymers204,76012
Non-polymers5238
Water00
1
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*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*AP*CP*AP*TP*GP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,64210
Polymers102,3806
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Tumor protein 63
H: Tumor protein 63
I: Tumor protein 63
J: Tumor protein 63
K: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
L: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,64210
Polymers102,3806
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.739, 180.544, 98.174
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number5
Space group name H-MC121

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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.: 8 / 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*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'


Mass: 5826.822 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: p63 Response Element with 1-bp Overlapping Half Sites (strand 1)
#3: DNA chain 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'


Mass: 5817.808 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: p63 Response Element with 1-bp Overlapping Half Sites (strand 2)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2 M ammonium formate, 0.1 M Bis-Tris, pH 6.8, 12% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03320357 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2011 / 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: 4.2→99.788 Å / Num. all: 15264 / Num. obs: 14781 / % possible obs: 96.8 % / Observed criterion σ(F): 1.45 / Observed criterion σ(I): 1.6 / Redundancy: 2.8 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 5.8
Reflection shellResolution: 4.2→4.3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1142 / % possible all: 94.6

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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 / Resolution: 4.2→59.869 Å / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 33.7 / Stereochemistry target values: Engh & Huber / Details: REFINED WITH PSEUDO-MEROHEDRAL TWINNING
RfactorNum. reflection% reflectionSelection details
Rfree0.3342 769 5.2 %RANDOM
Rwork0.326 ---
obs0.3402 14781 96.87 %-
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.3 e/Å3
Refinement stepCycle: LAST / Resolution: 4.2→59.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11656 1546 8 0 13210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01813664
X-RAY DIFFRACTIONf_angle_d1.74718894
X-RAY DIFFRACTIONf_dihedral_angle_d21.2695244
X-RAY DIFFRACTIONf_chiral_restr0.1122104
X-RAY DIFFRACTIONf_plane_restr0.0092220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.5230.39041500.37722694X-RAY DIFFRACTION90
4.523-4.97570.31421370.332748X-RAY DIFFRACTION91
4.9757-5.69010.35471660.33372781X-RAY DIFFRACTION92
5.6901-7.14770.39311340.36972853X-RAY DIFFRACTION94
7.1477-27.37330.32831570.31782912X-RAY DIFFRACTION94
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)
10.61570.08470.40110.3173-0.06260.35710.3326-0.1246-1.10590.07340.1688-0.22490.585-0.86670.09481.4462-0.1474-0.12851.8394-0.28231.594131.1935-13.286227.6878
20.39120.117-0.68080.172-0.14060.6677-0.20530.2928-0.18290.37270.16220.35240.2949-0.1304-0.00171.50350.05670.01953.26-0.1632.4983-31.196612.678427.7876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain B or chain C or chain D or chain E or chain F
2X-RAY DIFFRACTION2chain G or chain H or chain I or chain J or chain K or chain L

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