5ZJR

Structure of AbdB/Exd complex bound to a 'Magenta14' DNA sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.

Zeiske, T.Baburajendran, N.Kaczynska, A.Brasch, J.Palmer, A.G.Shapiro, L.Honig, B.Mann, R.S.

(2018) Cell Rep 24: 2221-2230

  • DOI: https://doi.org/10.1016/j.celrep.2018.07.100
  • Primary Citation of Related Structures:  
    5ZJQ, 5ZJR, 5ZJS, 5ZJT

  • PubMed Abstract: 

    Transcription factors bind to their binding sites over a wide range of affinities, yet how differences in affinity are encoded in DNA sequences is not well understood. Here, we report X-ray crystal structures of four heterodimers of the Hox protein AbdominalB bound with its cofactor Extradenticle to four target DNA molecules that differ in affinity by up to ∼20-fold. Remarkably, despite large differences in affinity, the overall structures are very similar in all four complexes. In contrast, the predicted shapes of the DNA binding sites (i.e., the intrinsic DNA shape) in the absence of bound protein are strikingly different from each other and correlate with affinity: binding sites that must change conformations upon protein binding have lower affinities than binding sites that have more optimal conformations prior to binding. Together, these observations suggest that intrinsic differences in DNA shape provide a robust mechanism for modulating affinity without affecting other protein-DNA interactions.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homeobox protein abdominal-B84Drosophila melanogasterMutation(s): 0 
Gene Names: Abd-BCG10291
UniProt
Find proteins for P09087 (Drosophila melanogaster)
Explore P09087 
Go to UniProtKB:  P09087
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09087
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Homeobox protein extradenticle74Drosophila melanogasterMutation(s): 0 
Gene Names: exdCG8933
UniProt
Find proteins for P40427 (Drosophila melanogaster)
Explore P40427 
Go to UniProtKB:  P40427
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UniProt GroupP40427
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*CP*GP*TP*AP*AP*AP*TP*CP*AP*TP*GP*C)-3')14Drosophila melanogaster
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*CP*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*AP*C)-3')14Drosophila melanogaster
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.33α = 90
b = 49.445β = 109.18
c = 95.092γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-19
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references