4FP9

Human MTERF4-NSUN4 protein complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

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This is version 1.1 of the entry. See complete history. 


Literature

Structure of the human MTERF4-NSUN4 protein complex that regulates mitochondrial ribosome biogenesis.

Spahr, H., Habermann, B., Gustafsson, C.M., Larsson, N.G., Hallberg, B.M.

(2012) Proc Natl Acad Sci U S A 109: 15253-15258

  • DOI: 10.1073/pnas.1210688109
  • Primary Citation of Related Structures:  
    4FP9

  • PubMed Abstract: 

    • Proteins crucial for the respiratory chain are translated by the mitochondrial ribosome. Mitochondrial ribosome biogenesis is therefore critical for oxidative phosphorylation capacity and disturbances are known to cause human disease. This complex proces ...

    Proteins crucial for the respiratory chain are translated by the mitochondrial ribosome. Mitochondrial ribosome biogenesis is therefore critical for oxidative phosphorylation capacity and disturbances are known to cause human disease. This complex process is evolutionary conserved and involves several RNA processing and modification steps required for correct ribosomal RNA maturation. We recently showed that a member of the mitochondrial transcription termination factor (MTERF) family of proteins, MTERF4, recruits NSUN4, a 5-methylcytosine RNA methyltransferase, to the large ribosomal subunit in a process crucial for mitochondrial ribosome biogenesis. Here, we describe the 3D crystal structure of the human MTERF4-NSUN4 complex determined to 2.9 Å resolution. MTERF4 is composed of structurally repeated MTERF-motifs that form a nucleic acid binding domain. NSUN4 lacks an N- or C-terminal extension that is commonly used for RNA recognition by related RNA methyltransferases. Instead, NSUN4 binds to the C-terminus of MTERF4. A positively charged surface forms an RNA binding path from the concave to the convex side of MTERF4 and further along NSUN4 all of the way into the active site. This finding suggests that both subunits of the protein complex likely contribute to RNA recognition. The interface between MTERF4 and NSUN4 contains evolutionarily conserved polar and hydrophobic amino acids, and mutations that change these residues completely disrupt complex formation. This study provides a molecular explanation for MTERF4-dependent recruitment of NSUN4 to ribosomal RNA and suggests a unique mechanism by which other members of the large MTERF-family of proteins can regulate ribosomal biogenesis.

    Organizational Affiliation: 

    Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
methyltransferase NSUN4 A, C, D, F360Homo sapiensMutation(s): 0 
Gene Names: NSUN4
EC: 2.1.1
Find proteins for Q96CB9 (Homo sapiens)
Explore Q96CB9 
Go to UniProtKB:  Q96CB9
NIH Common Fund Data Resources
PHAROS:  Q96CB9
GTEx:  ENSG00000117481
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
mTERF domain-containing protein 2 B, E, G, H335Homo sapiensMutation(s): 0 
Gene Names: HSPC096, MTERFD2, MTERF4
Find proteins for Q7Z6M4 (Homo sapiens)
Explore Q7Z6M4 
Go to UniProtKB:  Q7Z6M4
NIH Common Fund Data Resources
PHAROS:  Q7Z6M4
GTEx:  ENSG00000122085
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.76α = 90
b = 82.27β = 90
c = 507.57γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
SHARPphasing
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references