3HTS

HEAT SHOCK TRANSCRIPTION FACTOR/DNA COMPLEX

• PDB DOI:  https://doi.org/10.2210/pdb3HTS/pdb
• NAKB: 3HTS

• Classification: TRANSCRIPTION/DNA
• Organism(s): Kluyveromyces lactis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-11-16 Released: 1999-04-29 
• Deposition Author(s): Littlefield, O., Nelson, H.C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.245 
• R-Value Work: 0.208 

Literature

A new use for the 'wing' of the 'winged' helix-turn-helix motif in the HSF-DNA cocrystal.

Littlefield, O., Nelson, H.C.

(1999) Nat Struct Biol 6: 464-470

• PubMed: 10331875 
• DOI: https://doi.org/10.1038/8269
• Primary Citation of Related Structures:  
  3HTS


• PubMed Abstract: 
  

The 1.75 A crystal structure of the Kluyveromyces lactis heat shock transcription factor (HSF) DNA-binding domain (DBD) complexed with DNA reveals a protein-DNA interface with few direct major groove contacts and a number of phosphate backbone contacts that are primarily water-mediated interactions. The DBD, a 'winged' helix-turn-helix protein, displays a novel mode of binding in that the 'wing' does not contact DNA like all others of that class. Instead, the monomeric DBD, which crystallized as a symmetric dimer to a pair of nGAAn inverted repeats, uses the 'wing' to form part of the protein-protein contacts. This dimer interface is likely important for increasing the DNA-binding specificity and affinity of the trimeric form of HSF, as well as for increasing cooperativity between adjacent trimers.

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Related Citations: 

• Refinedsolution Structure and Dynamics of the DNA-Binding Domain of the Heat Shock Factor from Kluyveromyces Lactis
  Damberger, F.F., Pelton, J.G., Liu, C., Cho, H., Harrison, C.J., Nelson, H.C.M., Wemmer, D.E.
  (1995) J Mol Biol 254: 704

• Crystal Structure of the DNA Binding Domain of the Heat Shock Transcription Factor
  Harrison, C.J., Bohm, A.A., Nelson, H.C.M.
  (1994) Science 263: 224

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Organizational Affiliation: 

Department of Molecular and Cell Biology, University of California, Berkeley 94720-3206, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.7 kDa 
• Atom Count: 1,023 
• Modelled Residue Count: 94 
• Deposited Residue Count: 114 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT SHOCK TRANSCRIPTION FACTOR	B	102	Kluyveromyces lactis	Mutation(s): 0
UniProt
Find proteins for P22121 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore P22121  Go to UniProtKB:  P22121

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3'	A	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.245 
• R-Value Work: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.69	α = 90
b = 54.9	β = 122.44
c = 41.06	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-29 
Deposition Author(s): Littlefield, O., Nelson, H.C.M.

Revision History  

• Version 1.0: 1999-04-29
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description