4FZV

Crystal structure of the human MTERF4:NSUN4:SAM ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9996 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Essential MTERF4:NSUN4 Protein Complex Reveals How an MTERF Protein Collaborates to Facilitate rRNA Modification.

Yakubovskaya, E.Guja, K.E.Mejia, E.Castano, S.Hambardjieva, E.Choi, W.S.Garcia-Diaz, M.

(2012) Structure 20: 1940-1947

  • DOI: 10.1016/j.str.2012.08.027

  • PubMed Abstract: 
  • MTERF4 is the first MTERF family member shown to bind RNA and plays an essential role as a regulator of ribosomal biogenesis in mammalian mitochondria. It forms a complex with the rRNA methyltransferase NSUN4 and recruits it to the large ribosomal su ...

    MTERF4 is the first MTERF family member shown to bind RNA and plays an essential role as a regulator of ribosomal biogenesis in mammalian mitochondria. It forms a complex with the rRNA methyltransferase NSUN4 and recruits it to the large ribosomal subunit. In this article, we characterize the interaction between both proteins, demonstrate that MTERF4 strongly stimulates the specificity of NSUN4 during in vitro methylation experiments, and present the 2.0 Å resolution crystal structure of the MTERF4:NSUN4 protein complex, lacking 48 residues of the MTERF4 C-terminal acidic tail, bound to S-adenosyl-L-methionine, thus revealing the nature of the interaction between both proteins and the structural conservation of the most divergent of the human MTERF family members. Moreover, the structure suggests a model for RNA binding by the MTERF4:NSUN4 complex, providing insight into the mechanism by which an MTERF family member facilitates rRNA methylation.


    Organizational Affiliation

    Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative methyltransferase NSUN4
A
359Homo sapiensMutation(s): 0 
Gene Names: NSUN4
EC: 2.1.1.-
Find proteins for Q96CB9 (Homo sapiens)
Go to Gene View: NSUN4
Go to UniProtKB:  Q96CB9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
mTERF domain-containing protein 2
B
239Homo sapiensMutation(s): 0 
Gene Names: MTERF4 (MTERFD2)
Find proteins for Q7Z6M4 (Homo sapiens)
Go to Gene View: MTERF4
Go to UniProtKB:  Q7Z6M4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
B
L-PEPTIDE LINKINGC4 H9 N O2

--

MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9996 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 298.667α = 90.00
b = 53.226β = 98.75
c = 52.963γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
SHARPphasing
SCALAdata scaling
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2012-10-17
    Type: Database references
  • Version 1.2: 2012-11-28
    Type: Database references