4FZV | pdb_00004fzv

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.190 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.str.2012.08.027
  • Primary Citation Related Structures: 
    4FZV

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 68.16 kDa 
  • Atom Count: 4,635 
  • Modeled Residue Count: 575 
  • Deposited Residue Count: 598 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative methyltransferase NSUN4359Homo sapiensMutation(s): 0 
Gene Names: NSUN4
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96CB9 (Homo sapiens)
Explore Q96CB9 
Go to UniProtKB:  Q96CB9
PHAROS:  Q96CB9
GTEx:  ENSG00000117481 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96CB9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
mTERF domain-containing protein 2239Homo sapiensMutation(s): 0 
Gene Names: MTERFD2HSPC096
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z6M4 (Homo sapiens)
Explore Q7Z6M4 
Go to UniProtKB:  Q7Z6M4
PHAROS:  Q7Z6M4
GTEx:  ENSG00000122085 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z6M4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
UNK
Query on UNK
B
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.190 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 298.667α = 90
b = 53.226β = 98.75
c = 52.963γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
SHARPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references
  • Version 1.2: 2012-11-28
    Changes: Database references
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary