7BB3

Structure of S. pombe YG-box oligomer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Identification and structural analysis of the Schizosaccharomyces pombe SMN complex.

Veepaschit, J.Viswanathan, A.Bordonne, R.Grimm, C.Fischer, U.

(2021) Nucleic Acids Res 49: 7207-7223

  • DOI: https://doi.org/10.1093/nar/gkab158
  • Primary Citation of Related Structures:  
    7BB3, 7BBL

  • PubMed Abstract: 

    The macromolecular SMN complex facilitates the formation of Sm-class ribonucleoproteins involved in mRNA processing (UsnRNPs). While biochemical studies have revealed key activities of the SMN complex, its structural investigation is lagging behind. Here we report on the identification and structural determination of the SMN complex from the lower eukaryote Schizosaccharomyces pombe, consisting of SMN, Gemin2, 6, 7, 8 and Sm proteins. The core of the SMN complex is formed by several copies of SMN tethered through its C-terminal alpha-helices arranged with alternating polarity. This creates a central platform onto which Gemin8 binds and recruits Gemins 6 and 7. The N-terminal parts of the SMN molecules extrude via flexible linkers from the core and enable binding of Gemin2 and Sm proteins. Our data identify the SMN complex as a multivalent hub where Sm proteins are collected in its periphery to allow their joining with UsnRNA.


  • Organizational Affiliation

    Department of Biochemistry, Biocenter, University of Würzburg, Würzburg 97074, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Survival motor neuron-like protein 1,Survival motor neuron-like protein 1
A, B
69Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: smn1yab8SPAC2G11.08c
UniProt
Find proteins for Q09808 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q09808 
Go to UniProtKB:  Q09808
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09808
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.19α = 90
b = 83.71β = 90
c = 160.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFi573/7-2, 8-2

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Derived calculations
  • Version 1.2: 2021-03-31
    Changes: Database references
  • Version 1.3: 2021-07-28
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Database references, Refinement description