1IHF | pdb_00001ihf

INTEGRATION HOST FACTOR/DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1IHF/pdb
• NAKB: 1IHF

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1996-08-21 Released: 1997-02-12 
• Deposition Author(s): Rice, P.A., Yang, S.-W., Mizuuchi, K., Nash, H.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.255 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 

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: 8980235 
• DOI: https://doi.org/10.1016/s0092-8674(00)81824-3
• Primary Citation 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. 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.22 kDa 
• Atom Count: 3,337 
• Modeled Residue Count: 260 
• Deposited Residue Count: 263 
• Unique protein chains: 2
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (INTEGRATION HOST FACTOR (ALPHA) (IHF))	D [auth A]	99	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A6X7 (Escherichia coli (strain K12)) Explore P0A6X7  Go to UniProtKB:  P0A6X7

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (INTEGRATION HOST FACTOR (BETA) (IHF))	E [auth B]	94	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A6Y1 (Escherichia coli (strain K12)) Explore P0A6Y1  Go to UniProtKB:  P0A6Y1

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (35-MER)	A [auth C]	35	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3')	B [auth D]	15	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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]	20	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	F [auth C], G [auth C], H [auth C], I [auth C], J [auth C], K [auth D], L [auth D], M [auth D], N [auth E], O [auth A], P [auth A], Q [auth A], R [auth B], S [auth B], T [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.255 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.36	α = 90
b = 59.92	β = 90
c = 180.8	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
RAVE	model building
X-PLOR	refinement
HKL	data reduction
SCALEPACK	data scaling
RAVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-02-12 
Deposition Author(s): Rice, P.A., Yang, S.-W., Mizuuchi, K., Nash, H.A.

Revision History  

• 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
• Version 1.6: 2024-02-07
  Changes: Data collection, Database references, Derived calculations