1IHF

INTEGRATION HOST FACTOR/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


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


  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (INTEGRATION HOST FACTOR (ALPHA) (IHF))
A
99Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ihfA (hid, himA)
Find proteins for P0A6X7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6X7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (INTEGRATION HOST FACTOR (BETA) (IHF))
B
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ihfB (himD, hip)
Find proteins for P0A6Y1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6Y1
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (35-MER)C35N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3')D15N/A
Entity ID: 3
MoleculeChainsLengthOrganism
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')E20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
A, B, C, D, E
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.360α = 90.00
b = 59.920β = 90.00
c = 180.800γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
X-PLORrefinement
SCALEPACKdata scaling
HKLdata reduction
RAVEmodel building
RAVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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