1IHF

INTEGRATION HOST FACTOR/DNA COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.192 

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This is version 1.5 of the entry. See complete history. 


Literature

Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn.

Rice, P.A., Yang, S., Mizuuchi, K., Nash, H.A.

(1996) Cell 87: 1295-1306

  • DOI: https://doi.org/10.1016/s0092-8674(00)81824-3
  • Primary Citation of Related Structures:  
    1IHF

  • PubMed Abstract: 

    • Integration host factor (IHF) is a small heterodimeric protein that specifically binds to DNA and functions as an architectural factor in many cellular processes in prokaryotes. Here, we report the crystal structure of IHF complexed with 35 bp of DNA. The DNA is wrapped around the protein and bent by >160 degrees, thus reversing the direction of the helix axis within a very short distance ...

    Integration host factor (IHF) is a small heterodimeric protein that specifically binds to DNA and functions as an architectural factor in many cellular processes in prokaryotes. Here, we report the crystal structure of IHF complexed with 35 bp of DNA. The DNA is wrapped around the protein and bent by >160 degrees, thus reversing the direction of the helix axis within a very short distance. Much of the bending occurs at two large kinks where the base stacking is interrupted by intercalation of a proline residue. IHF contacts the DNA exclusively via the phosphodiester backbone and the minor groove and relies heavily on indirect readout to recognize its binding sequence. One such readout involves a six-base A tract, providing evidence for the importance of a narrow minor groove.

    Organizational Affiliation: 

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (INTEGRATION HOST FACTOR (ALPHA) (IHF))D [auth A]99Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A6X7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A6X7
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UniProt GroupP0A6X7
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (INTEGRATION HOST FACTOR (BETA) (IHF))E [auth B]94Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A6Y1 (Escherichia coli (strain K12))
Explore P0A6Y1 
Go to UniProtKB:  P0A6Y1
Entity Groups  
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UniProt GroupP0A6Y1
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (35-MER)A [auth C]35N/A
Protein Feature View
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3')B [auth D]15N/A
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*C P*AP*CP*C)-3')C [auth E]20N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.36α = 90
b = 59.92β = 90
c = 180.8γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
RAVEmodel building
X-PLORrefinement
HKLdata reduction
SCALEPACKdata scaling
RAVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-05-02
    Changes: Derived calculations, Refinement description
  • Version 1.4: 2012-05-09
    Changes: Refinement description
  • Version 1.5: 2019-05-01
    Changes: Data collection, Refinement description