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- PDB-4g82: Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a F... -

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Basic information

Entry
Database: PDB / ID: 4g82
TitleCrystal Structure of p73 DNA-Binding Domain Tetramer bound to a Full Response-Element
Components
  • DNA (5'-D(P*GP*AP*AP*CP*AP*TP*GP*TP*TP*C)-3')
  • Tumor protein p73P73
KeywordsDNA binding protein/DNA / beta-immunoglobulin like fold / TUMOR SUPPRESSOR / dna / 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 / mismatch repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / cell cycle / positive regulation of apoptotic process / 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 / metal ion binding / nucleus / 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: 3.1 Å
AuthorsEthayathulla, A.S. / Viadiu, H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a Full Response-Element
Authors: Ethayathulla, A.S. / Viadiu, H.
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Derived calculations
Revision 1.2Jul 17, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name / _software.version
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 p73
B: Tumor protein p73
E: DNA (5'-D(P*GP*AP*AP*CP*AP*TP*GP*TP*TP*C)-3')
F: DNA (5'-D(P*GP*AP*AP*CP*AP*TP*GP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7716
Polymers53,6404
Non-polymers1312
Water28816
1
A: Tumor protein p73
B: Tumor protein p73
E: DNA (5'-D(P*GP*AP*AP*CP*AP*TP*GP*TP*TP*C)-3')
F: DNA (5'-D(P*GP*AP*AP*CP*AP*TP*GP*TP*TP*C)-3')
hetero molecules

A: Tumor protein p73
B: Tumor protein p73
E: DNA (5'-D(P*GP*AP*AP*CP*AP*TP*GP*TP*TP*C)-3')
F: DNA (5'-D(P*GP*AP*AP*CP*AP*TP*GP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,54212
Polymers107,2808
Non-polymers2624
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Unit cell
Length a, b, c (Å)175.472, 175.472, 34.317
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 / P73 / p53-like transcription factor / p53-related protein


Mass: 23775.955 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: human, P73, TP73 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15350
#2: DNA chain DNA (5'-D(P*GP*AP*AP*CP*AP*TP*GP*TP*TP*C)-3')


Mass: 3044.017 Da / Num. of mol.: 2 / Source method: obtained synthetically
#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.: 16 / 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: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 298 K / pH: 9
Details: 0.1M TRIS, 20% PEG3350 , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2011 / Details: MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 11516 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 16.7

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VD0

3vd0


Resolution: 3.1→43.87 Å / SU ML: 0.42 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Phase error: 30.47 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rfree0.268 248 4.8 %
Rwork0.238 --
obs0.24 11319 99.3 %
all-11516 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.2 Å2
Baniso -1Baniso -2Baniso -3
1-9.25 Å20 Å20 Å2
2--9.25 Å20 Å2
3----18.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.1→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 410 2 16 3576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123694
X-RAY DIFFRACTIONf_angle_d2.1575104
X-RAY DIFFRACTIONf_dihedral_angle_d21.7511423
X-RAY DIFFRACTIONf_chiral_restr0.089557
X-RAY DIFFRACTIONf_plane_restr0.013605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1028-3.4150.35131370.29352596X-RAY DIFFRACTION98
3.415-3.90890.31221330.27272664X-RAY DIFFRACTION100
3.9089-4.92370.2681410.22632698X-RAY DIFFRACTION100
4.9237-43.87240.22091320.21222818X-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)
10.08160.0486-0.06050.2812-0.060.1365-0.23810.16540.1193-0.1244-0.2491-0.4413-0.0795-0.0511-0.4024-0.89510.27760.7474-0.043-0.1014-0.470811.8355-77.9061-7.4746
20.13680.04220.02420.12590.14410.1153-0.11040.04490.3369-0.177-0.03990.2397-0.5874-0.2332-0.1137-0.28240.4350.3353-0.0195-0.3988-0.2792-26.7204-61.29452.4066
30.02430.0054-0.01550.01160.00330.01620.0231-0.03270.08770.0020.0487-0.01090.0084-0.03730.02280.4971-0.18690.21810.49560.0060.1104-1.3686-54.6442-3.2553
40.02970.0092-0.02050.0158-0.00420.01360.09940.11740.0716-0.03080.05230.0428-0.0658-0.01840.02250.44170.03240.04130.3342-0.01450.0675-1.0469-54.6786-2.1771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND (RESID 112:312 OR RESID 401:401 OR RESID 501:508 ) )
2X-RAY DIFFRACTION2(CHAIN B AND (RESID 113:312 OR RESID 401:401 OR RESID 501:508 ) )
3X-RAY DIFFRACTION3(CHAIN E AND (RESID 400:409 OR RESID 501:501 ) )
4X-RAY DIFFRACTION4(CHAIN F AND (RESID 410:419 OR RESID 501:501 ) )
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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