4NWB

Crystal structure of Mrt4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle.

Leidig, C.Thoms, M.Holdermann, I.Bradatsch, B.Berninghausen, O.Bange, G.Sinning, I.Hurt, E.Beckmann, R.

(2014) Nat Commun 5: 3491-3491

  • DOI: 10.1038/ncomms4491
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • During eukaryotic ribosome biogenesis, nascent ribosomal RNA (rRNA) forms pre-ribosomal particles containing ribosomal proteins and assembly factors. Subsequently, these immature rRNAs are processed and remodelled. Little is known about the premature ...

    During eukaryotic ribosome biogenesis, nascent ribosomal RNA (rRNA) forms pre-ribosomal particles containing ribosomal proteins and assembly factors. Subsequently, these immature rRNAs are processed and remodelled. Little is known about the premature assembly states of rRNAs and their structural rearrangement during ribosome biogenesis. Using cryo-EM we characterize a pre-60S particle, where the 5S rRNA and its associated ribosomal proteins L18 and L5 (5S ribonucleoprotein (RNP)) are rotated by almost 180° when compared with the mature subunit. Consequently, neighbouring 25S rRNA helices that protrude from the base of the central protuberance are deformed. This altered topology is stabilized by nearby assembly factors (Rsa4 and Nog1), which were identified by fitting their three-dimensional structures into the cryo-EM density. We suggest that the 5S RNP performs a semicircular movement during 60S biogenesis to adopt its final position, fulfilling a chaperone-like function in guiding the flanking 25S rRNA helices of the central protuberance to their final topology.


    Organizational Affiliation

    Gene Center and Center of Integrated Protein Science Munich (CiPS-M), Department of Chemistry and Biochemistry, University of Munich, 81377 Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRNA turnover protein 4
A
278Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S616 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S616
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 61.292α = 90.00
b = 65.271β = 111.03
c = 71.404γ = 90.00
Software Package:
Software NamePurpose
AutoSolphasing
PHENIXrefinement
XDSdata reduction
ADSCdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Database references