5XJR

Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with SmD1(1-82)/D2/F/E/G from Human


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Negative cooperativity between Gemin2 and RNA provides insights into RNA selection and the SMN complex's release in snRNP assembly.

Yi, H.Mu, L.Shen, C.Kong, X.Wang, Y.Hou, Y.Zhang, R.

(2019) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkz1135
  • Primary Citation of Related Structures:  
    5XJQ, 5XJR, 5XJS

  • PubMed Abstract: 
  • The assembly of snRNP cores, in which seven Sm proteins, D1/D2/F/E/G/D3/B, form a ring around the nonameric Sm site of snRNAs, is the early step of spliceosome formation and essential to eukaryotes. It is mediated by the PMRT5 and SMN complexes sequentially in vivo ...

    The assembly of snRNP cores, in which seven Sm proteins, D1/D2/F/E/G/D3/B, form a ring around the nonameric Sm site of snRNAs, is the early step of spliceosome formation and essential to eukaryotes. It is mediated by the PMRT5 and SMN complexes sequentially in vivo. SMN deficiency causes neurodegenerative disease spinal muscular atrophy (SMA). How the SMN complex assembles snRNP cores is largely unknown, especially how the SMN complex achieves high RNA assembly specificity and how it is released. Here we show, using crystallographic and biochemical approaches, that Gemin2 of the SMN complex enhances RNA specificity of SmD1/D2/F/E/G via a negative cooperativity between Gemin2 and RNA in binding SmD1/D2/F/E/G. Gemin2, independent of its N-tail, constrains the horseshoe-shaped SmD1/D2/F/E/G from outside in a physiologically relevant, narrow state, enabling high RNA specificity. Moreover, the assembly of RNAs inside widens SmD1/D2/F/E/G, causes the release of Gemin2/SMN allosterically and allows SmD3/B to join. The assembly of SmD3/B further facilitates the release of Gemin2/SMN. This is the first to show negative cooperativity in snRNP assembly, which provides insights into RNA selection and the SMN complex's release. These findings reveal a basic mechanism of snRNP core assembly and facilitate pathogenesis studies of SMA.


    Organizational Affiliation

    Department of Ophthalmology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, P.R. China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gem-associated protein 2A [auth 2]241Homo sapiensMutation(s): 0 
Gene Names: GEMIN2SIP1
UniProt & NIH Common Fund Data Resources
Find proteins for O14893 (Homo sapiens)
Explore O14893 
Go to UniProtKB:  O14893
PHAROS:  O14893
GTEx:  ENSG00000092208 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14893
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1B [auth A]82Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
UniProt & NIH Common Fund Data Resources
Find proteins for P62314 (Homo sapiens)
Explore P62314 
Go to UniProtKB:  P62314
PHAROS:  P62314
GTEx:  ENSG00000167088 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62314
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2C [auth B]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
UniProt & NIH Common Fund Data Resources
Find proteins for P62316 (Homo sapiens)
Explore P62316 
Go to UniProtKB:  P62316
PHAROS:  P62316
GTEx:  ENSG00000125743 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62316
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein ED [auth E]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
UniProt & NIH Common Fund Data Resources
Find proteins for P62304 (Homo sapiens)
Explore P62304 
Go to UniProtKB:  P62304
PHAROS:  P62304
GTEx:  ENSG00000182004 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62304
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FE [auth F]86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
UniProt & NIH Common Fund Data Resources
Find proteins for P62306 (Homo sapiens)
Explore P62306 
Go to UniProtKB:  P62306
PHAROS:  P62306
GTEx:  ENSG00000139343 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62306
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GF [auth G]76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
UniProt & NIH Common Fund Data Resources
Find proteins for P62308 (Homo sapiens)
Explore P62308 
Go to UniProtKB:  P62308
PHAROS:  P62308
GTEx:  ENSG00000143977 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62308
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Survival motor neuron proteinG [auth M]37Homo sapiensMutation(s): 0 
Gene Names: SMN1SMNSMNTSMN2SMNC
UniProt & NIH Common Fund Data Resources
Find proteins for Q16637 (Homo sapiens)
Explore Q16637 
Go to UniProtKB:  Q16637
PHAROS:  Q16637
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16637
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.96α = 90
b = 114.12β = 90
c = 130.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2017-05-04 
  • Released Date: 2018-07-04 
  • Deposition Author(s): Yi, H., Zhang, R.

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references