5XJL

Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with SmD1/D2/F/E/G from Human

  • Classification: SPLICING
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-05-02 Released: 2018-05-02 
  • Deposition Author(s): Zhang, R.
  • Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


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Literature

Structure of a key intermediate of the SMN complex reveals Gemin2's crucial function in snRNP assembly

Zhang, R.So, B.R.Li, P.Yong, J.Glisovic, T.Wan, L.Dreyfuss, G.

(2011) Cell 146: 384-395

  • DOI: 10.1016/j.cell.2011.06.043
  • Primary Citation of Related Structures:  
    5XJL

  • PubMed Abstract: 
  • The SMN complex mediates the assembly of heptameric Sm protein rings on small nuclear RNAs (snRNAs), which are essential for snRNP function. Specific Sm core assembly depends on Sm proteins and snRNA recognition by SMN/Gemin2- and Gemin5-containing subunits, respectively ...

    The SMN complex mediates the assembly of heptameric Sm protein rings on small nuclear RNAs (snRNAs), which are essential for snRNP function. Specific Sm core assembly depends on Sm proteins and snRNA recognition by SMN/Gemin2- and Gemin5-containing subunits, respectively. The mechanism by which the Sm proteins are gathered while preventing illicit Sm assembly on non-snRNAs is unknown. Here, we describe the 2.5 Å crystal structure of Gemin2 bound to SmD1/D2/F/E/G pentamer and SMN's Gemin2-binding domain, a key assembly intermediate. Remarkably, through its extended conformation, Gemin2 wraps around the crescent-shaped pentamer, interacting with all five Sm proteins, and gripping its bottom and top sides and outer perimeter. Gemin2 reaches into the RNA-binding pocket, preventing RNA binding. Interestingly, SMN-Gemin2 interaction is abrogated by a spinal muscular atrophy (SMA)-causing mutation in an SMN helix that mediates Gemin2 binding. These findings provide insight into SMN complex assembly and specificity, linking snRNP biogenesis and SMA pathogenesis.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6148, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gem-associated protein 2A [auth 2]280Homo sapiensMutation(s): 0 
Gene Names: GEMIN2SIP1
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1B [auth A]119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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PHAROS:  P62314
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2C [auth B]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein ED [auth E]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Find proteins for P62304 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FE [auth F]86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GF [auth G]76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Find proteins for P62308 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Survival motor neuron proteinG [auth M]37Homo sapiensMutation(s): 0 
Gene Names: SMN1SMNSMNTSMN2SMNC
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.83α = 90
b = 84.6β = 90
c = 104.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-02 
  • Released Date: 2018-05-02 
  • Deposition Author(s): Zhang, R.
  • This entry supersedes: 3S6N

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570720
National Natural Science Foundation of ChinaChina81441109

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release