3MVA

Crystal structure of human MTERF1 bound to the termination sequence

• PDB DOI: https://doi.org/10.2210/pdb3MVA/pdb
• NAKB: 3MVA

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-03 Released: 2010-06-30 
• Deposition Author(s): Yakubovskaya, E., Mejia, E., Byrnes, J., Hambardjieva, E., Garcia-Diaz, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.244 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Literature

Helix unwinding and base flipping enable human MTERF1 to terminate mitochondrial transcription.

Yakubovskaya, E., Mejia, E., Byrnes, J., Hambardjieva, E., Garcia-Diaz, M.

(2010) Cell 141: 982-993

• PubMed: 20550934 
• DOI: https://doi.org/10.1016/j.cell.2010.05.018
• Primary Citation of Related Structures:  
  3MVA, 3MVB


• PubMed Abstract: 
  

  Defects in mitochondrial gene expression are associated with aging and disease. Mterf proteins have been implicated in modulating transcription, replication and protein synthesis. We have solved the structure of a member of this family, the human mitochondrial transcriptional terminator MTERF1, bound to dsDNA containing the termination sequence. The structure indicates that upon sequence recognition MTERF1 unwinds the DNA molecule, promoting eversion of three nucleotides. Base flipping is critical for stable binding and transcriptional termination. Additional structural and biochemical results provide insight into the DNA binding mechanism and explain how MTERF1 recognizes its target sequence. Finally, we have demonstrated that the mitochondrial pathogenic G3249A and G3244A mutations interfere with key interactions for sequence recognition, eliminating termination. Our results provide insight into the role of mterf proteins and suggest a link between mitochondrial disease and the regulation of mitochondrial transcription.

---

Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.83 kDa 
• Atom Count: 3,620 
• Modelled Residue Count: 368 
• Deposited Residue Count: 387 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription termination factor, mitochondrial	A [auth O]	343	Homo sapiens	Mutation(s): 0  Gene Names: MTERF, MTERF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99551 (Homo sapiens) Explore Q99551  Go to UniProtKB:  Q99551
GTEx:  ENSG00000127989

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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]	22	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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]	22	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.244 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.631	α = 90
b = 89.709	β = 90
c = 161.293	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-30 
Deposition Author(s): Yakubovskaya, E., Mejia, E., Byrnes, J., Hambardjieva, E., Garcia-Diaz, M.

Revision History  

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references