[English] 日本語
Yorodumi
- PDB-3vd2: structure of p73 DNA binding domain tetramer modulates p73 transa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vd2
Titlestructure of p73 DNA binding domain tetramer modulates p73 transactivation
Components
  • DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
  • Tumor protein p73
KeywordsANTITUMOR PROTEIN/DNA / PROTEIN DNA COMPLEX / beta-immunoglobulin-like fold / TUMOUR SUPPRESSOR / DNA / ANTITUMOR 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 / TP53 Regulates Transcription of Caspase Activators and Caspases / 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 / positive regulation of oligodendrocyte differentiation / 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 / TP53 Regulates Transcription of Caspase Activators and Caspases / 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 / positive regulation of oligodendrocyte differentiation / 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 / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / positive regulation of MAPK cascade / regulation of cell cycle / ciliary basal body / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / centrosome / DNA damage response / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / 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. / Tse, P.W. / Nguyen, S. / Viadiu, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of p73 DNA-binding domain tetramer modulates p73 transactivation.
Authors: Ethayathulla, A.S. / Tse, P.W. / Monti, P. / Nguyen, S. / Inga, A. / Fronza, G. / Viadiu, H.
History
DepositionJan 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
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
Revision 1.3Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tumor protein p73
B: Tumor protein p73
C: Tumor protein p73
D: Tumor protein p73
I: Tumor protein p73
J: Tumor protein p73
E: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
F: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
G: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
H: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
L: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
K: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,72718
Polymers168,33512
Non-polymers3926
Water00
1
A: Tumor protein p73
B: Tumor protein p73
C: Tumor protein p73
D: Tumor protein p73
E: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
F: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
G: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
H: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,48512
Polymers112,2238
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Tumor protein p73
J: Tumor protein p73
L: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
K: DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2426
Polymers56,1124
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.400, 91.127, 137.475
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe octamer in the ASU corresponds to a tetramer p73DBD plus four chains of two continuous DNA double strands. Additionally, the tetramer in the ASU corresponds to a dimer p73DBD plus two chains of one continuous DNA double strand.

-
Components

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


Mass: 23775.955 Da / Num. of mol.: 6 / Fragment: unp residues 115-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O15350
#2: DNA chain
DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')


Mass: 4279.804 Da / Num. of mol.: 6 / Source method: obtained synthetically
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-tris, 0.1M Ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.5

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2010 / Details: mirror
RadiationMonochromator: Rh coated flat mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 97649 / Num. obs: 16649 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rsym value: 0.12 / Net I/σ(I): 10.6
Reflection shellResolution: 4→4.14 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 1695 / Rsym value: 0.4 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3KMD

3kmd


Resolution: 4→45.69 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 55733.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 350 2.1 %RANDOM
Rwork0.248 ---
all0.258 16649 --
obs0.248 16648 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.0964 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 87.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å20 Å20.75 Å2
2--6.33 Å20 Å2
3----2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 4→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9480 1666 6 0 11152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d1.42
LS refinement shellResolution: 4→4.25 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 69 2.5 %
Rwork0.278 2691 -
obs-2691 99.5 %
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more