Anabaena HU-DNA cocrystal structure (AHU2)

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1093/emboj/cdg351
  • Primary Citation of Related Structures:  
    1P51, 1P71, 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, 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.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-binding protein HUC [auth A],
D [auth B]
94Anabaena sp.Mutation(s): 0 
Gene Names: HUP OR HANA OR ASR3935
Find proteins for P05514 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P05514 
Go to UniProtKB:  P05514
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05514
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
B [auth D]
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DNA PDBBind:  1P78 Kd: 3.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.43α = 90
b = 91.81β = 90
c = 100.75γ = 90
Software Package:
Software NamePurpose
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: 2003-05-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Refinement description