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

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Basic information

Entry
Database: PDB / ID: 3qyn
TitleStructure of p63 DNA Binding Domain in Complex with a 22 Base Pair A/T Rich Response Element Containing 2 Base Pair Spacer Between Half Sites
Components
  • 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*TP*AP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
  • Tumor protein 63Neoplasm
KeywordsTRANSCRIPTION ACTIVATOR/DNA / B DNA double helix / protein-DNA complex / zinc binding / beta sandwich / greek key / transcription factor / DNA binding / 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 / 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 / proximal/distal pattern formation / 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 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 / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / establishment of skin barrier / Pyroptosis / positive regulation of osteoblast differentiation / keratinocyte differentiation / MDM2/MDM4 family protein binding / Notch signaling pathway / 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 / 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 / DNA damage response / chromatin binding / dendrite / 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 / 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: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structures of p63 DNA binding domain in complexes with half-site and with spacer-containing full response elements.
Authors: Chen, C. / Gorlatova, N. / Kelman, Z. / Herzberg, O.
History
DepositionMar 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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*TP*AP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'
F: 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*TP*AP*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
Water8,413467
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.984, 140.984, 119.346
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 / 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: 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: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II (DE3) / References: UniProt: Q9H3D4
#2: DNA chain 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*TP*AP*AP*AP*AP*CP*AP*TP*GP*TP*TP*T)-3'


Mass: 6748.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: contains a consensus P63 binding motif
#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 / Water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 3.28 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% 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
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 3, 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→85.346 Å / Num. all: 46625 / Num. obs: 46625 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 45.73 Å2 / Rsym value: 0.09 / Net I/σ(I): 20.1
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 3473 / Rsym value: 0.483 / % possible all: 100

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QYM

3qym


Resolution: 2.5→61.048 Å / SU ML: 0.41 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 26.84 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 2384 5.12 %RANDOM
Rwork0.2103 ---
obs0.2121 46601 99.91 %-
all-46625 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.008 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 58.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.1847 Å20 Å2-0 Å2
2--6.1847 Å2-0 Å2
3----12.3694 Å2
Refinement stepCycle: LAST / Resolution: 2.5→61.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 896 4 467 7333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117128
X-RAY DIFFRACTIONf_angle_d1.6359882
X-RAY DIFFRACTIONf_dihedral_angle_d24.7384264
X-RAY DIFFRACTIONf_chiral_restr0.11099
X-RAY DIFFRACTIONf_plane_restr0.0071149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5510.36061340.34362578X-RAY DIFFRACTION100
2.551-2.60650.31171510.32592604X-RAY DIFFRACTION100
2.6065-2.66710.35241340.32892609X-RAY DIFFRACTION100
2.6671-2.73380.37381430.32732556X-RAY DIFFRACTION100
2.7338-2.80780.38521350.32782614X-RAY DIFFRACTION100
2.8078-2.89040.33081530.30642582X-RAY DIFFRACTION100
2.8904-2.98370.31531340.28472603X-RAY DIFFRACTION100
2.9837-3.09030.33081630.26852546X-RAY DIFFRACTION100
3.0903-3.2140.23411300.23072621X-RAY DIFFRACTION100
3.214-3.36030.22571140.20812619X-RAY DIFFRACTION100
3.3603-3.53740.2831420.21632584X-RAY DIFFRACTION100
3.5374-3.7590.22151390.20552586X-RAY DIFFRACTION100
3.759-4.04920.23481280.1962620X-RAY DIFFRACTION100
4.0492-4.45660.18951380.162610X-RAY DIFFRACTION100
4.4566-5.10120.17591460.14492615X-RAY DIFFRACTION100
5.1012-6.42590.21461550.15942611X-RAY DIFFRACTION100
6.4259-61.0660.19661450.16472659X-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)
11.1415-0.7583-0.52621.98861.26381.06180.15030.1812-0.0352-0.5056-0.26290.2041-0.3568-0.2275-00.39210.0805-0.08670.2455-0.01650.3035-59.22756.473722.3836
20.8566-0.5860.12211.54530.51411.46610.02960.1612-0.0133-0.1953-0.19380.0286-0.2131-0.033900.28590.0302-0.01150.2592-0.01370.3065-48.8382-19.7896-10.6794
31.19450.81470.49490.83950.84550.96680.3577-0.59250.18270.5618-0.44950.2960.3562-0.3381-00.4303-0.1970.13240.4703-0.12170.4321-57.026520.2341-43.7339
40.85670.5411-0.15991.03010.80451.09660.2467-0.3543-0.00950.4523-0.41480.05070.4928-0.3505-00.4778-0.14760.04350.4101-0.03490.2688-36.221639.4474-10.2521
5-0.1780.3249-0.81650.9076-2.27361.1160.0252-0.0034-0.0499-0.21440.10850.05340.17120.37060.00010.693-0.14580.03950.38290.04190.2664-36.07218.2202-10.4483
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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