4CYC

CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE HEXAPEPTIDE AND UBDA MOTIFS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/Pbc Interaction Mode.

Foos, N.Maurel-Zaffran, C.Mate, M.J.Vincentelli, R.Hainaut, M.Berenger, H.Pradel, J.Saurin, A.J.Ortiz-Lombardia, M.Graba, Y.

(2015) Structure 23: 270

  • DOI: https://doi.org/10.1016/j.str.2014.12.011
  • Primary Citation of Related Structures:  
    4CYC, 4UUS, 4UUT

  • PubMed Abstract: 

    The patterning function of Hox proteins relies on assembling protein complexes with PBC proteins, which often involves a protein motif found in most Hox proteins, the so-called Hexapeptide (HX). Hox/PBC complexes likely gained functional diversity by acquiring additional modes of interaction. Here, we structurally characterize the first HX alternative interaction mode based on the paralogue-specific UbdA motif and further functionally validate structure-based predictions. The UbdA motif folds as a flexible extension of the homeodomain recognition helix and defines Hox/PBC contacts that occur, compared with those mediated by the HX motif, on the opposing side of the DNA double helix. This provides a new molecular facet to Hox/PBC complex assembly and suggests possible mechanisms for the diversification of Hox protein function.


  • Organizational Affiliation

    Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HOMEOTIC PROTEIN ULTRABITHORAX93Drosophila melanogasterMutation(s): 0 
UniProt
Find proteins for P83949 (Drosophila melanogaster)
Explore P83949 
Go to UniProtKB:  P83949
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83949
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HOMEOBOX PROTEIN EXTRADENTICLE76Drosophila melanogasterMutation(s): 0 
UniProt
Find proteins for P40427 (Drosophila melanogaster)
Explore P40427 
Go to UniProtKB:  P40427
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40427
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP)-3'15Drosophila melanogaster
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*GP)-3'15Drosophila melanogaster
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.707α = 90
b = 97.707β = 90
c = 73.735γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
TRUNCATEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description