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- PDB-4g83: Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a F... -

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Basic information

Entry
Database: PDB / ID: 4g83
TitleCrystal Structure of p73 DNA-Binding Domain Tetramer bound to a Full Response-Element
Components
  • Tumor protein p73P73
  • dna
KeywordsDNA BINDING PROTEIN/DNA / BETA-IMMUNOGLOBULIN FOLD / TUMOR SUPPRESSOR / 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 / regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release ...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 / regulation of mitotic cell cycle / 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 / 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 / DNA (> 10) / Tumor protein p73
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 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.classification / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
E: dna
F: dna
A: Tumor protein p73
B: Tumor protein p73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9536
Polymers59,8224
Non-polymers1312
Water0
1
E: dna
F: dna
A: Tumor protein p73
B: Tumor protein p73
hetero molecules

E: dna
F: dna
A: Tumor protein p73
B: Tumor protein p73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,90512
Polymers119,6448
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Unit cell
Length a, b, c (Å)141.717, 96.345, 34.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.583392, -0.811872, 0.022757), (-0.810884, 0.583813, 0.040357), (-0.046051, 0.005091, -0.998926)-62.88351, -33.21291, 16.33878

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Components

#1: DNA chain dna /


Mass: 6134.966 Da / Num. of mol.: 2 / Fragment: unp residues 115-312 / Source method: obtained synthetically / Details: dna synthesized
#2: Protein Tumor protein p73 / P73 / p53-like transcription factor / p53-related protein


Mass: 23775.955 Da / Num. of mol.: 2
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
#3: 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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M BTP, 20% PEG3350 , pH 7.5, 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 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2012 / Details: mirror
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 8957 / Num. obs: 5072 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.88

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vd0

3vd0


Resolution: 4→45.61 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.887 / SU ML: 0.39 / Isotropic thermal model: TLS refinement / σ(F): 1.35 / Phase error: 28.13 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rfree0.3073 202 4.64 %
Rwork0.2414 --
obs0.2443 4349 99.82 %
all-5072 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.022 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--5.45 Å20 Å2
3----5.92 Å2
Refinement stepCycle: LAST / Resolution: 4→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 410 2 0 3506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0313640
X-RAY DIFFRACTIONf_angle_d3.0625032
X-RAY DIFFRACTIONf_dihedral_angle_d20.9141402
X-RAY DIFFRACTIONf_chiral_restr0.1552
X-RAY DIFFRACTIONf_plane_restr0.014594
LS refinement shellResolution: 4.0002→45.6125 Å
RfactorNum. reflection% reflection
Rfree0.3073 202 -
Rwork0.2414 4147 -
obs--100 %
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)
12.0375-0.69191.06362.6688-0.72981.8812-0.2864-0.00781.4485-1.14290.4491-0.3277-0.11340.28760.57640.34830.3152-0.05550.54830.51180.7995-22.7571-32.75219.3385
25.066-0.4275-2.37381.64890.91622.5592-0.52330.4095-0.5928-0.5105-0.2792-0.17551.34920.0305-0.25661.33440.1660.08330.60770.06440.5611-22.7099-32.74078.032
32.1681.1984-0.43068.4996-3.92272.8918-0.5420.2087-0.4675-0.674-0.4141-2.91980.18130.5368-0.31650.1596-0.257-0.10570.3177-0.07770.1433-11.4072-8.005113.2438
43.5469-2.5135-0.95977.32341.87992.981-0.1748-0.4719-2.03141.7329-0.33544.4161-0.2336-0.15390.0291-0.0088-0.0335-0.49260.4532-0.1318-1.2789-49.4701-28.08073.7272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND RESID 400:409 )E400 - 409
2X-RAY DIFFRACTION2( CHAIN F AND RESID 410:419 )F410 - 419
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1:310 )A1 - 310
4X-RAY DIFFRACTION4( CHAIN B AND RESID 113:310 )B113 - 310

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