7N40

Crystal structure of LIN9-RbAp48-LIN37, a MuvB subcomplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


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Literature

The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes.

Asthana, A.Ramanan, P.Hirschi, A.Guiley, K.Z.Wijeratne, T.U.Shelansky, R.Doody, M.J.Narasimhan, H.Boeger, H.Tripathi, S.Muller, G.A.Rubin, S.M.

(2022) Nat Commun 13: 526-526

  • DOI: https://doi.org/10.1038/s41467-022-28094-1
  • Primary Citation of Related Structures:  
    7N40

  • PubMed Abstract: 

    The chromatin architecture in promoters is thought to regulate gene expression, but it remains uncertain how most transcription factors (TFs) impact nucleosome position. The MuvB TF complex regulates cell-cycle dependent gene-expression and is critical for differentiation and proliferation during development and cancer. MuvB can both positively and negatively regulate expression, but the structure of MuvB and its biochemical function are poorly understood. Here we determine the overall architecture of MuvB assembly and the crystal structure of a subcomplex critical for MuvB function in gene repression. We find that the MuvB subunits LIN9 and LIN37 function as scaffolding proteins that arrange the other subunits LIN52, LIN54 and RBAP48 for TF, DNA, and histone binding, respectively. Biochemical and structural data demonstrate that MuvB binds nucleosomes through an interface that is distinct from LIN54-DNA consensus site recognition and that MuvB increases nucleosome occupancy in a reconstituted promoter. We find in arrested cells that MuvB primarily associates with a tightly positioned +1 nucleosome near the transcription start site (TSS) of MuvB-regulated genes. These results support a model that MuvB binds and stabilizes nucleosomes just downstream of the TSS on its target promoters to repress gene expression.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-binding protein RBBP4425Homo sapiensMutation(s): 0 
Gene Names: RBBP4RBAP48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09028 (Homo sapiens)
Explore Q09028 
Go to UniProtKB:  Q09028
PHAROS:  Q09028
GTEx:  ENSG00000162521 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09028
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Protein lin-9 homolog180Homo sapiensMutation(s): 0 
Gene Names: LIN9BARATGS
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TKA1 (Homo sapiens)
Explore Q5TKA1 
Go to UniProtKB:  Q5TKA1
PHAROS:  Q5TKA1
GTEx:  ENSG00000183814 
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UniProt GroupQ5TKA1
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein lin-37 homolog39Homo sapiensMutation(s): 0 
Gene Names: LIN37MSTP064
UniProt & NIH Common Fund Data Resources
Find proteins for Q96GY3 (Homo sapiens)
Explore Q96GY3 
Go to UniProtKB:  Q96GY3
PHAROS:  Q96GY3
GTEx:  ENSG00000267796 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96GY3
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.58α = 90
b = 77.81β = 114.71
c = 64.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM124148

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description