5FD3

Structure of Lin54 tesmin domain bound to DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


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

Literature

Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters.

Marceau, A.H., Felthousen, J.G., Goetsch, P.D., Iness, A.N., Lee, H.W., Tripathi, S.M., Strome, S., Litovchick, L., Rubin, S.M.

(2016) Nat Commun 7: 12301-12301

  • DOI: 10.1038/ncomms12301

  • PubMed Abstract: 

    • The MuvB complex recruits transcription factors to activate or repress genes with cell cycle-dependent expression patterns. MuvB contains the DNA-binding protein LIN54, which directs the complex to promoter cell cycle genes homology region (CHR) elem ...

    The MuvB complex recruits transcription factors to activate or repress genes with cell cycle-dependent expression patterns. MuvB contains the DNA-binding protein LIN54, which directs the complex to promoter cell cycle genes homology region (CHR) elements. Here we characterize the DNA-binding properties of LIN54 and describe the structural basis for recognition of a CHR sequence. We biochemically define the CHR consensus as TTYRAA and determine that two tandem cysteine rich regions are required for high-affinity DNA association. A crystal structure of the LIN54 DNA-binding domain in complex with a CHR sequence reveals that sequence specificity is conferred by two tyrosine residues, which insert into the minor groove of the DNA duplex. We demonstrate that this unique tyrosine-mediated DNA binding is necessary for MuvB recruitment to target promoters. Our results suggest a model in which MuvB binds near transcription start sites and plays a role in positioning downstream nucleosomes.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, California 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein lin-54 homolog
A, B
135Homo sapiensMutation(s): 0 
Gene Names: LIN54 (CXCDC1, KIAA2037)
Find proteins for Q6MZP7 (Homo sapiens)
Go to Gene View: LIN54
Go to UniProtKB:  Q6MZP7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*GP*TP*TP*TP*GP*AP*AP*AP*CP*T)-3')C,H12Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*GP*TP*TP*TP*CP*AP*AP*AP*CP*TP*C)-3')D,I13Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 39.320α = 98.40
b = 53.880β = 102.53
c = 67.120γ = 106.57
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
SCALAdata scaling
iMOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Derived calculations