5AFF

Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.398 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Symportin 1 Chaperones 5S Rnp Assembly During Ribosome Biogenesis by Occupying an Essential Rrna-Binding Site.

Calvino, F.R.Kharde, S.Ori, A.Hendricks, A.Wild, K.Kressler, D.Bange, G.Hurt, E.Beck, M.Sinning, I.

(2015) Nat.Commun. 6: 6510

  • DOI: 10.1038/ncomms7510

  • PubMed Abstract: 
  • During 60S biogenesis, mature 5S RNP consisting of 5S RNA, RpL5 and RpL11, assembles into a pre-60S particle, where docking relies on RpL11 interacting with helix 84 (H84) of the 25S RNA. How 5S RNP is assembled for recruitment into the pre-60S is no ...

    During 60S biogenesis, mature 5S RNP consisting of 5S RNA, RpL5 and RpL11, assembles into a pre-60S particle, where docking relies on RpL11 interacting with helix 84 (H84) of the 25S RNA. How 5S RNP is assembled for recruitment into the pre-60S is not known. Here we report the crystal structure of a ternary symportin Syo1-RpL5-N-RpL11 complex and provide biochemical and structural insights into 5S RNP assembly. Syo1 guards the 25S RNA-binding surface on RpL11 and competes with H84 for binding. Pull-down experiments show that H84 releases RpL11 from the ternary complex, but not in the presence of 5S RNA. Crosslinking mass spectrometry visualizes structural rearrangements on incorporation of 5S RNA into the Syo1-RpL5-RpL11 complex supporting the formation of a pre-5S RNP. Our data underline the dual role of Syo1 in ribosomal protein transport and as an assembly platform for 5S RNP.


    Organizational Affiliation

    Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany.,European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SYMPORTIN 1
A
654Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S5S6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S5S6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L5
B
48Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SEG2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SEG2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L11
C
173Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SHQ2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SHQ2
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.398 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.087α = 90.00
b = 105.959β = 90.00
c = 147.234γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHENIXphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release