4F7U

The 6S snRNP assembly intermediate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.898 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 

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:  

  • 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 ch ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
A, C
119Mus musculusMutation(s): 0 
Gene Names: Snrpd1
Find proteins for P62315 (Mus musculus)
Go to UniProtKB:  P62315
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
B, D
118Mus musculusMutation(s): 0 
Gene Names: Snrpd2
Find proteins for P62317 (Mus musculus)
Go to UniProtKB:  P62317
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
E, H
92Mus musculusMutation(s): 0 
Gene Names: Snrpe
Find proteins for P62305 (Mus musculus)
Go to UniProtKB:  P62305
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
F, I
86Xenopus laevisMutation(s): 0 
Gene Names: snrpf
Find proteins for P62321 (Xenopus laevis)
Go to UniProtKB:  P62321
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
G, J
76Mus musculusMutation(s): 0 
Gene Names: Snrpg
Find proteins for P62309 (Mus musculus)
Go to UniProtKB:  P62309
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Methylosome subunit pICln
Q, P
129Drosophila melanogasterMutation(s): 1 
Gene Names: icln
Find proteins for A1ZAW5 (Drosophila melanogaster)
Go to UniProtKB:  A1ZAW5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G
Download SDF File 
Download CCD File 
H
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.898 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 180.720α = 90.00
b = 65.298β = 92.47
c = 99.346γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History 

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