5CRK

Crystal Structure of the MTERF1 F243A substitution bound to the termination sequence.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion.

Byrnes, J.Hauser, K.Norona, L.Mejia, E.Simmerling, C.Garcia-Diaz, M.

(2016) J Mol Biol 428: 2542-2556

  • DOI: https://doi.org/10.1016/j.jmb.2015.10.021
  • Primary Citation of Related Structures:  
    5CKY, 5CO0, 5CRJ, 5CRK

  • PubMed Abstract: 

    Human mitochondrial transcription termination occurs within the leu-tRNA gene and is mediated by the DNA binding protein MTERF1. The crystal structure of MTERF1 bound to the canonical termination sequence reveals a rare base flipping event that involves the eversion of three nucleotides. These nucleotides are stabilized by stacking interactions with three MTERF1 residues, which are essential not only for base flipping but also for termination activity. To further understand the mechanism of base flipping, we examined each of the individual stacking interactions in structural, energetic and functional detail. Individual substitutions of Arg162, Tyr288 and Phe243 have revealed unequal contributions to overall termination activity. Furthermore, our work identifies an important role for Phe322 in the base flipping mechanism and we demonstrate how Phe322 and Phe243 are important for coupling base flipping between the heavy and light strand DNA chains. We propose a stepwise model for the base flipping process that recapitulates our observations. Finally, we show that MTERF1 has the ability to accommodate alternate active conformations. The adaptability of base flipping has implications for MTERF1 function and for the putative function of MTERF1 at alternative binding sites in human mitochondria.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination factor 1, mitochondrialA [auth O]324Homo sapiensMutation(s): 1 
Gene Names: MTERF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99551 (Homo sapiens)
Explore Q99551 
Go to UniProtKB:  Q99551
GTEx:  ENSG00000127989 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99551
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*TP*AP*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*CP*AP*TP*CP*TP*TP*A)-3')B [auth D]22Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*AP*AP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*GP*TP*AP*AP*T)-3')C [auth E]22Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.743α = 90
b = 89.375β = 90
c = 159.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesR00-ES015421
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM100021
United Mitochondrial Disease FoundationUnited StatesUMDF to M.G.D.
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM092714

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description