4WAN

Crystal structure of Msl5 protein in complex with RNA at 1.8 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis for recognition of intron branchpoint RNA by yeast Msl5 and selective effects of interfacial mutations on splicing of yeast pre-mRNAs.

Jacewicz, A.Chico, L.Smith, P.Schwer, B.Shuman, S.

(2015) RNA 21: 401-414

  • DOI: 10.1261/rna.048942.114
  • Primary Citation of Related Structures:  
    4WAN, 4WAL

  • PubMed Abstract: 
  • Saccharomyces cerevisiae Msl5 orchestrates spliceosome assembly by binding the intron branchpoint sequence 5'-UACUAAC and, with its heterodimer partner protein Mud2, establishing cross intron-bridging interactions with the U1 snRNP at the 5' splice site. Here we define the central Msl5 KH-QUA2 domain as sufficient for branchpoint RNA recognition ...

    Saccharomyces cerevisiae Msl5 orchestrates spliceosome assembly by binding the intron branchpoint sequence 5'-UACUAAC and, with its heterodimer partner protein Mud2, establishing cross intron-bridging interactions with the U1 snRNP at the 5' splice site. Here we define the central Msl5 KH-QUA2 domain as sufficient for branchpoint RNA recognition. The 1.8 Å crystal structure of Msl5-(KH-QUA2) bound to the branchpoint highlights an extensive network of direct and water-mediated protein-RNA and intra-RNA atomic contacts at the interface that illuminate how Msl5 recognizes each nucleobase of the UACUAAC element. The Msl5 structure rationalizes a large body of mutational data and inspires new functional studies herein, which reveal how perturbations of the Msl5·RNA interface impede the splicing of specific yeast pre-mRNAs. We also identify interfacial mutations in Msl5 that bypass the essentiality of Sub2, a DExD-box ATPase implicated in displacing Msl5 from the branchpoint in exchange for the U2 snRNP. These studies establish an atomic resolution framework for understanding splice site selection and early spliceosome dynamics.


    Organizational Affiliation

    Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA bschwer@med.cornell.edu s-shuman@ski.mskcc.org.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Branchpoint-bridging proteinA, C, E, G129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MSL5BBPSF1YLR116WL2949
UniProt
Find proteins for Q12186 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12186 
Go to UniProtKB:  Q12186
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')B, D, F, H11N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.80 Å
    • R-Value Free: 0.206 
    • R-Value Work: 0.175 
    • R-Value Observed: 0.180 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 53.38α = 90
    b = 130.97β = 117.43
    c = 53.37γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM52470
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM50288

    Revision History  (Full details and data files)

    • Version 1.0: 2014-12-17
      Type: Initial release
    • Version 1.1: 2015-01-28
      Changes: Database references
    • Version 1.2: 2015-03-04
      Changes: Database references
    • Version 1.3: 2017-09-06
      Changes: Advisory, Data collection, Database references, Derived calculations, Other, Source and taxonomy
    • Version 1.4: 2017-09-20
      Changes: Author supporting evidence
    • Version 1.5: 2019-12-25
      Changes: Author supporting evidence