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- PDB-5kbd: Structural Studies of Transcription Factor p73 DNA Binding Domain... -

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Basic information

Entry
Database: PDB / ID: 5kbd
TitleStructural Studies of Transcription Factor p73 DNA Binding Domain Bound to PA26 20-mer Response Element
Components
  • DNA (5'-D(P*AP*GP*AP*CP*TP*TP*GP*TP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*AP*CP*AP*AP*GP*TP*CP*T)-3')
  • Tumor protein p73
KeywordsDNA BINDING PROTEIN/DNA / tumor suppressor transcription factor p53 response element / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation ...positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / mismatch repair / MDM2/MDM4 family protein binding / response to organonitrogen compound / regulation of mitotic cell cycle / transcription corepressor binding / kidney development / protein tetramerization / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of MAPK cascade / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Tumour protein p73, 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 p73, 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 / Tumor protein p73
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNguyen, H.T. / Huang, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA009523 United States
CitationJournal: To Be Published
Title: Structural Studies of Transcription Factor p73 DNA Binding Domain Bound to PA26 20-mer Response Element
Authors: Nguyen, H.T. / Huang, D.
History
DepositionJun 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor protein p73
B: Tumor protein p73
C: DNA (5'-D(P*GP*GP*AP*CP*AP*AP*GP*TP*CP*T)-3')
D: DNA (5'-D(P*AP*GP*AP*CP*TP*TP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1196
Polymers52,9884
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.878, 174.878, 34.282
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Tumor protein p73 / p53-like transcription factor / p53-related protein


Mass: 23449.557 Da / Num. of mol.: 2 / Fragment: UNP residues 115-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP73, P73 / Production host: Escherichia coli (E. coli) / References: UniProt: O15350
#2: DNA chain DNA (5'-D(P*GP*GP*AP*CP*AP*AP*GP*TP*CP*T)-3')


Mass: 3069.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*AP*GP*AP*CP*TP*TP*GP*TP*CP*C)-3')


Mass: 3019.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 9.0, 50 mM Sodium Acetate, 16% (w/v) PEG 3350; 2:1 or 4:1 Protein:DNA ratio, 1:1 protein/DNA solution:well solution ratio

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→29.411 Å / Num. obs: 15238 / % possible obs: 99.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 20.26
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 1.48 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G82

4g82


Resolution: 2.8→29.411 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.51
Details: Simulated annealing, XYZ and B-factor refinement through CNS 1.3. XYZ, B-factor, and TLS refinement through PHENIX.
RfactorNum. reflection% reflection
Rfree0.3076 729 9.98 %
Rwork0.2788 --
obs0.2817 15157 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 410 2 0 3584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033712
X-RAY DIFFRACTIONf_angle_d0.5465126
X-RAY DIFFRACTIONf_dihedral_angle_d18.6962186
X-RAY DIFFRACTIONf_chiral_restr0.043558
X-RAY DIFFRACTIONf_plane_restr0.003610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-2.89060.49191360.44291230X-RAY DIFFRACTION99
2.8906-2.99390.41071360.39311199X-RAY DIFFRACTION99
2.9939-3.11360.39631450.40561257X-RAY DIFFRACTION100
3.1136-3.25510.42111310.40061208X-RAY DIFFRACTION100
3.2551-3.42650.3561390.35111231X-RAY DIFFRACTION97
3.4265-3.64080.36021320.33011210X-RAY DIFFRACTION100
3.6408-3.92130.3311410.31151252X-RAY DIFFRACTION100
3.9213-4.31490.28121350.26981261X-RAY DIFFRACTION100
4.3149-4.93670.24241390.23471253X-RAY DIFFRACTION99
4.9367-6.21010.26941370.21231238X-RAY DIFFRACTION98
6.2101-29.41250.26261410.21151306X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -7.2846 Å / Origin y: -67.557 Å / Origin z: -2.5744 Å
111213212223313233
T0.2723 Å2-0.019 Å2-0.034 Å2-0.3801 Å2-0.0616 Å2--0.1653 Å2
L1.9347 °2-0.4266 °2-0.9774 °2-1.6826 °2-0.0222 °2--0.7056 °2
S-0.0198 Å °0.2038 Å °0.1481 Å °-0.0524 Å °-0.0704 Å °-0.0826 Å °-0.0567 Å °0.0216 Å °0.0301 Å °
Refinement TLS groupSelection details: all

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