1FYL

SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA IN A HEAD-TO-HEAD ORIENTATION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex.

Littlefield, O., Nelson, H.C.

(2001) Proteins 45: 219-228

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • We present here three high-resolution crystal structures of complexes between the DNA-binding domain of the heat-shock transcription factor (HSF) and DNA oligomers. Although the DNA oligomers contain HSF's specific binding sequence, called a heat-sho ...

    We present here three high-resolution crystal structures of complexes between the DNA-binding domain of the heat-shock transcription factor (HSF) and DNA oligomers. Although the DNA oligomers contain HSF's specific binding sequence, called a heat-shock element, the crystal structures do not contain the specific protein-DNA complex. In one crystal structure, the 10 base pair DNA oligomer is statically disordered. In the other two related structures, the 12 base pair DNA oligomers are in unique positions, but the protein-DNA contacts in these two crystals are not sequence specific. In all three structures, the DNA appears to act as a rigid, polyanion scaffold to support columns of proteins in a crystalline lattice. A robust crystal packing interface between protein monomers obscures the true DNA-binding surface, known from previous genetic and biochemical studies. By redesigning the protein to interfere with the crystal lattice contacts, we were able to obtain physiologically relevant crystals in a specific protein-DNA complex. Thus, a crystal-packing interface was able to prevent the weak, but physiological relevant interactions between a protein and DNA.

    Related Citations: 
    • A new use for the 'wing' of the 'winged' helix-turn-helix motif in the HSF-DNA cocrystal
      Littlefield, O.,Nelson, H.C.M.
      (1999) Nat.Struct.Mol.Biol. 6: 464

    Organizational Affiliation: 

    Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HEAT SHOCK FACTOR PROTEIN
A, B
92Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 3 
Gene Names: HSF
Find proteins for P22121 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  P22121
Entity ID: 1
MoleculeChainsLengthOrganism
HEAD-TO-HEAD HSEC,D12N/A
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
C, D
DNA LINKINGC9 H12 Br N2 O8 PDU
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.140α = 90.00
b = 33.730β = 118.35
c = 77.840γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
DENZOdata reduction
CCP4data scaling
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-28
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance