1VTN

CO-CRYSTAL STRUCTURE OF THE HNF-3/FORK HEAD DNA-RECOGNITION MOTIF RESEMBLES HISTONE H5

• PDB DOI: https://doi.org/10.2210/pdb1VTN/pdb
• NAKB: 1VTN

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1995-01-06 Released: 2011-07-13 
• Deposition Author(s): Clark, K.L., Halay, E.D., Lai, E., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

Literature

Co-Crystal Structure of the HNF-3/Fork Head DNA-Recognition Motif Resembles Histone H5

Clark, K.L., Halay, E.D., Lai, E., Burley, S.K.

(1993) Nature 364: 412-420

• PubMed: 8332212 
• DOI: https://doi.org/10.1038/364412a0
• Primary Citation of Related Structures:  
  1VTN


• PubMed Abstract: 
  

  The three-dimensional structure of an HNF-3/fork head DNA-recognition motif complexed with DNA has been determined by X-ray crystallography at 2.5 A resolution. This alpha/beta protein binds B-DNA as a monomer, through interactions with the DNA backbone and through both direct and water-mediated major and minor groove base contacts, inducing a 13 degrees bend. The transcription factor fold is very similar to the structure of histone H5. In its amino-terminal half, three alpha-helices adopt a compact structure that presents the third helix to the major groove. The remainder of the protein includes a twisted, antiparallel beta-structure and random coil that interacts with the minor groove.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, Rockefeller University, New York, New York 10021.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.02 kDa 
• Atom Count: 1,381 
• Modelled Residue Count: 128 
• Deposited Residue Count: 128 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HNF-3/FORK HEAD DNA-RECOGNITION MOTIF	C	102	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P55318 (Homo sapiens) Explore P55318  Go to UniProtKB:  P55318
PHAROS:  P55318 GTEx:  ENSG00000170608

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*CP*TP*AP*AP*GP*TP*CP*AP*AP*CP*C)-3')	A	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*TP*TP*GP*AP*CP*TP*TP*AP*GP*TP*C)-3')	B	13	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.6	α = 90
b = 74.6	β = 90
c = 85.05	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Clark, K.L., Halay, E.D., Lai, E., Burley, S.K.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references