1P71

Anabaena HU-DNA corcrystal structure (TR3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Flexible DNA bending in HU-DNA cocrystal structures

Swinger, K.S.Lemberg, K.M.Zhang, Y.Rice, P.A.

(2003) Embo J. 22: 3749-3760

  • DOI: 10.1093/emboj/cdg351
  • Primary Citation of Related Structures:  1P51, 1P78

  • PubMed Abstract: 
  • HU and IHF are members of a family of prokaryotic proteins that interact with the DNA minor groove in a sequence-specific (IHF) or non-specific (HU) manner to induce and/or stabilize DNA bending. HU plays architectural roles in replication initiation ...

    HU and IHF are members of a family of prokaryotic proteins that interact with the DNA minor groove in a sequence-specific (IHF) or non-specific (HU) manner to induce and/or stabilize DNA bending. HU plays architectural roles in replication initiation, transcription regulation and site-specific recombination, and is associated with bacterial nucleoids. Cocrystal structures of Anabaena HU bound to DNA (1P71, 1P78, 1P51) reveal that while underlying proline intercalation and asymmetric charge neutralization mechanisms of DNA bending are similar for IHF and HU, HU stabilizes different DNA bend angles ( approximately 105-140 degrees ). The two bend angles within a single HU complex are not coplanar, and the resulting dihedral angle is consistent with negative supercoiling. Comparison of HU-DNA and IHF-DNA structures suggests that sharper bending is correlated with longer DNA binding sites and smaller dihedral angles. An HU-induced bend may be better modeled as a hinge, not a rigid bend. The ability to induce or stabilize varying bend angles is consistent with HU's role as an architectural cofactor in many different systems that may require differing geometries.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-binding protein HU
A, B
94Nostoc sp. (strain PCC 7120 / UTEX 2576)Gene Names: hup (hanA)
Find proteins for P05514 (Nostoc sp. (strain PCC 7120 / UTEX 2576))
Go to UniProtKB:  P05514
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3'C,D21N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.441α = 90.00
b = 93.062β = 90.00
c = 100.342γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
EPMRphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance