5ZJQ

Structure of AbdB/Exd complex bound to a 'Red14' DNA sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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; Department of Systems Biology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA. Electronic address: rsm10@columbia.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein abdominal-BA84Drosophila melanogasterMutation(s): 0 
Gene Names: Abd-BCG10291
UniProt
Find proteins for P09087 (Drosophila melanogaster)
Explore P09087 
Go to UniProtKB:  P09087
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein extradenticleB74Drosophila melanogasterMutation(s): 0 
Gene Names: exdCG8933
UniProt
Find proteins for P40427 (Drosophila melanogaster)
Explore P40427 
Go to UniProtKB:  P40427
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*AP*TP*GP*C)-3')C14Drosophila melanogaster
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*TP*TP*AP*TP*GP*AP*C)-3')D14Drosophila melanogaster
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.056α = 90
b = 49.44β = 109.33
c = 95.194γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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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