1JB6

Crystal Structure of Dimerization Domain (1-33) of HNF-1alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The dimerization domain of HNF-1alpha: structure and plasticity of an intertwined four-helix bundle with application to diabetes mellitus.

Narayana, N.Hua, Q.Weiss, M.A.

(2001) J Mol Biol 310: 635-658

  • DOI: 10.1006/jmbi.2001.4780
  • Primary Citation of Related Structures:  
    1JB6

  • PubMed Abstract: 
  • Maturity-onset diabetes mellitus of the young (MODY) is a human genetic syndrome most commonly due to mutations in hepatocyte nuclear factor-1alpha (HNF-1alpha). Here, we describe the crystal structure of the HNF-1alpha dimerization domain at 1.7 A resolution and assess its structural plasticity ...

    Maturity-onset diabetes mellitus of the young (MODY) is a human genetic syndrome most commonly due to mutations in hepatocyte nuclear factor-1alpha (HNF-1alpha). Here, we describe the crystal structure of the HNF-1alpha dimerization domain at 1.7 A resolution and assess its structural plasticity. The crystal's low solvent content (23%, v/v) leads to tight packing of peptides in the lattice. Two independent dimers, similar in structure, are formed in the unit cell by a 2-fold crystallographic symmetry axis. The dimers define a novel intertwined four-helix bundle (4HB). Each protomer contains two alpha-helices separated by a sharp non-canonical turn. Dimer-related alpha-helices form anti-parallel coiled-coils, including an N-terminal "mini-zipper" complementary in structure, symmetry and surface characteristics to transcriptional coactivator dimerization cofactor of HNF-1 (DCoH). A confluence of ten leucine side-chains (five per protomer) forms a hydrophobic core. Isotope-assisted NMR studies demonstrate that a similar intertwined dimer exists in solution. Comparison of structures obtained in multiple independent crystal forms indicates that the mini-zipper is a stable structural element, whereas the C-terminal alpha-helix can adopt a broad range of orientations. Segmental alignment of the mini-zipper (mean pairwise root-mean-square difference (rmsd) in C(alpha) coordinates of 0.29 A) is associated with a 2.1 A mean C(alpha) rmsd displacement of the C-terminal coiled-coil. The greatest C-terminal structural variation (4.1 A C(alpha) rmsd displacement) is observed in the DCoH-bound peptide. Diabetes-associated mutations perturb distinct structural features of the HNF-1alpha domain. One mutation (L12H) destabilizes the domain but preserves structural specificity. Adjoining H12 side-chains in a native-like dimer are predicted to alter the functional surface of the mini-zipper involved in DCoH recognition. The other mutation (G20R), by contrast, leads to a dimeric molten globule, as indicated by its 1H-NMR features and fluorescent binding of 1-anilino-8-naphthalene sulfonate. We propose that a glycine-specific turn configuration enables specific interactions between the mini-zipper and the C-terminal coiled-coil.


    Related Citations: 
    • Diabetes-Associated Mutations in a beta-Cell Transcription factor Destabilize an Antiparallel "Mini-Zipper" in a Dimerization Interface
      Hua, Q.X., Zhao, M., Narayana, N., Nakagawa, S.H., Jia, W., Weiss, M.A.
      (2000) Proc Natl Acad Sci U S A 97: 1999
    • Structural Basis of Dimerization, Coactivator Recognition and MODY3 Mutations in HNF-1alpha
      Rose, R.B., Bayle, J.H., Endrizzi, J.A., Cronk, J.D., Crabtree, G.R., Alber, T.
      (2000) Nat Struct Biol 7: 744
    • High-Resolution Structure of the HNF-1alpha Dimerization Domain
      Rose, R.B., Endrizzi, J.A., Cronk, J.D., Holton, J., Alber, T.
      (2000) Biochemistry 39: 15062
    • HNF1, A Homeoprotein Member of the Hepatic Transcription Regulatory Network
      Tronche, F., Yaniv, M.
      (1992) Bioessays 14: 579
    • Maturity-onset Diabetes of the Young (MODY), MODY Genes and Non-Insulin-Dependent Diabetes mellitus
      Velho, G., Froguel, P.
      (1997) Diabetes Metab 23: 34

    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4935, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEPATOCYTE NUCLEAR FACTOR 1-ALPHAA, B33N/AMutation(s): 3 
UniProt
Find proteins for P22361 (Mus musculus)
Explore P22361 
Go to UniProtKB:  P22361
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22361
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
NLE
Query on NLE
A, B L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.231 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.42α = 90
b = 42.19β = 90
c = 42.43γ = 90
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations