4F7U

The 6S snRNP assembly intermediate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural Basis of Assembly Chaperone- Mediated snRNP Formation.

Grimm, C., Chari, A., Pelz, J.P., Kuper, J., Kisker, C., Diederichs, K., Stark, H., Schindelin, H., Fischer, U.

(2013) Mol Cell 49: 692-703

  • DOI: 10.1016/j.molcel.2012.12.009
  • Primary Citation of Related Structures:  
    4F7U, 4V98

  • PubMed Abstract: 

    • Small nuclear ribonucleoproteins (snRNPs) represent key constituents of major and minor spliceosomes. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA, which forms in a step-wise and factor-mediated reaction. The assembly chaperone pICln initially mediates the formation of an otherwise unstable pentameric Sm protein unit ...

    Small nuclear ribonucleoproteins (snRNPs) represent key constituents of major and minor spliceosomes. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA, which forms in a step-wise and factor-mediated reaction. The assembly chaperone pICln initially mediates the formation of an otherwise unstable pentameric Sm protein unit. This so-called 6S complex docks subsequently onto the SMN complex, which removes pICln and enables the transfer of pre-assembled Sm proteins onto snRNA. X-ray crystallography and electron microscopy was used to investigate the structural basis of snRNP assembly. The 6S complex structure identifies pICln as an Sm protein mimic, which enables the topological organization of the Sm pentamer in a closed ring. A second structure of 6S bound to the SMN complex components SMN and Gemin2 uncovers a plausible mechanism of pICln elimination and Sm protein activation for snRNA binding. Our studies reveal how assembly factors facilitate formation of RNA-protein complexes in vivo.

    Organizational Affiliation: 

    Department of Biochemistry, Theodor Boveri Institute, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany. clemens.grimm@uni-wuerzburg.de



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1A, C119Mus musculusMutation(s): 0 
Gene Names: Snrpd1
UniProt
Find proteins for P62315 (Mus musculus)
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UniProt GroupP62315
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2B, D118Mus musculusMutation(s): 0 
Gene Names: Snrpd2
UniProt
Find proteins for P62317 (Mus musculus)
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UniProt GroupP62317
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EE,
F [auth H]		92Mus musculusMutation(s): 0 
Gene Names: Snrpe
UniProt
Find proteins for P62305 (Mus musculus)
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UniProt GroupP62305
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FG [auth F],
H [auth I]		86Xenopus laevisMutation(s): 0 
Gene Names: snrpf
UniProt
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UniProt GroupP62321
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GI [auth G],
J		76Mus musculusMutation(s): 0 
Gene Names: Snrpg
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Methylosome subunit pIClnL [auth P],
K [auth Q]		129Drosophila melanogasterMutation(s): 1 
Gene Names: CG4924, icln
UniProt
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UniProt GroupA1ZAW5
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G
Download Ideal Coordinates CCD File 
M [auth H]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.72α = 90
b = 65.298β = 92.47
c = 99.346γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-05-16 
  • Released Date: 2013-01-30 
    • Deposition Author(s): Grimm, C., Pelz, J.P.

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-03-13
    Changes: Database references
  • Version 1.2: 2015-01-28
    Changes: Structure summary
  • Version 1.3: 2017-08-09
    Changes: Refinement description, Source and taxonomy