3VD2 | pdb_00003vd2

structure of p73 DNA binding domain tetramer modulates p73 transactivation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 
    0.284 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure of p73 DNA-binding domain tetramer modulates p73 transactivation.

Ethayathulla, A.S.Tse, P.W.Monti, P.Nguyen, S.Inga, A.Fronza, G.Viadiu, H.

(2012) Proc Natl Acad Sci U S A 109: 6066-6071

  • DOI: https://doi.org/10.1073/pnas.1115463109
  • Primary Citation Related Structures: 
    3VD0, 3VD1, 3VD2

  • PubMed Abstract: 

    The transcription factor p73 triggers developmental pathways and overlaps stress-induced p53 transcriptional pathways. How p53-family response elements determine and regulate transcriptional specificity remains an unsolved problem. In this work, we have determined the first crystal structures of p73 DNA-binding domain tetramer bound to response elements with spacers of different length. The structure and function of the adaptable tetramer are determined by the distance between two half-sites. The structures with zero and one base-pair spacers show compact p73 DNA-binding domain tetramers with large tetramerization interfaces; a two base-pair spacer results in DNA unwinding and a smaller tetramerization interface, whereas a four base-pair spacer hinders tetramerization. Functionally, p73 is more sensitive to spacer length than p53, with one base-pair spacer reducing 90% of transactivation activity and longer spacers reducing transactivation to basal levels. Our results establish the quaternary structure of the p73 DNA-binding domain required as a scaffold to promote transactivation.


  • Organizational Affiliation
    • Laboratory of Structural Biochemistry, Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive 0378, La Jolla, CA 92093, USA.

Macromolecule Content 

  • Total Structure Weight: 168.73 kDa 
  • Atom Count: 11,152 
  • Modeled Residue Count: 1,291 
  • Deposited Residue Count: 1,344 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor protein p73210Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O15350 (Homo sapiens)
Explore O15350 
Go to UniProtKB:  O15350
PHAROS:  O15350
GTEx:  ENSG00000078900 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15350
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')14N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free:  0.284 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.4α = 90
b = 91.127β = 90.2
c = 137.475γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-29
    Changes: Database references
  • Version 1.4: 2024-10-30
    Changes: Structure summary