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 
  • R-Value Observed: 0.184 

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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
  • Primary Citation of Related Structures:  
    5FD3

  • 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) elements ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein lin-54 homologA, B135Homo sapiensMutation(s): 0 
Gene Names: LIN54, CXCDC1, KIAA2037
UniProt & NIH Common Fund Data Resources
Find proteins for Q6MZP7 (Homo sapiens)
Explore Q6MZP7 
Go to UniProtKB:  Q6MZP7
PHAROS:  Q6MZP7
GTEx:  ENSG00000189308 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MZP7
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*TP*TP*TP*GP*AP*AP*AP*CP*T)-3')C,
E [auth H]		12Homo sapiens
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*AP*GP*TP*TP*TP*CP*AP*AP*AP*CP*TP*C)-3')D,
F [auth I]		13Homo sapiens
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.32α = 98.4
b = 53.88β = 102.53
c = 67.12γ = 106.57
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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