3N7Q | pdb_00003n7q

Crystal structure of human mitochondrial mTERF fragment (aa 99-399) in complex with a 12-mer DNA encompassing the tRNALeu(UUR) binding sequence

• PDB DOI: https://doi.org/10.2210/pdb3N7Q/pdb
• NAKB: 3N7Q

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


• Deposited: 2010-05-27 Released: 2010-06-16 
• Deposition Author(s): Jimenez-Menendez, N., Fernandez-Millan, P., Rubio-Cosials, A., Arnan, C., Montoya, J., Jacobs, H.T., Bernado, P., Coll, M., Uson, I., Sola, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.278 (Depositor) 
• R-Value Work: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat.

Jimenez-Menendez, N., Fernandez-Millan, P., Rubio-Cosials, A., Arnan, C., Montoya, J., Jacobs, H.T., Bernado, P., Coll, M., Uson, I., Sola, M.

(2010) Nat Struct Mol Biol 17: 891-893

• PubMed: 20543826 
• DOI: https://doi.org/10.1038/nsmb.1859
• Primary Citation Related Structures: 
  3N6S, 3N7Q


• PubMed Abstract: 
  

  The regulation of mitochondrial DNA (mtDNA) processes is slowly being characterized at a structural level. We present here crystal structures of human mitochondrial regulator mTERF, a transcription termination factor also implicated in replication pausing, in complex with double-stranded DNA oligonucleotides containing the tRNA(Leu)(UUR) gene sequence. mTERF comprises nine left-handed helical tandem repeats that form a left-handed superhelix, the Zurdo domain.

---

Organizational Affiliation: 
• Institut de Biologia Molecular de Barcelona, Parc Cientific de Barcelona, Barcelona, Spain.

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: 43.23 kDa 
• Atom Count: 2,933 
• Modeled Residue Count: 322 
• Deposited Residue Count: 334 
• 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	310	Homo sapiens	Mutation(s): 0  Gene Names: MTERF
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
DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*G)-3')	B	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*C)-3')	C	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.278 (Depositor) 
• R-Value Work:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.851	α = 90
b = 99.851	β = 90
c = 39.6	γ = 120

Software Package:

Software Name	Purpose
EPMR	phasing
PHENIX	refinement
XDS	data reduction
SHELX	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-16 
Deposition Author(s): Jimenez-Menendez, N., Fernandez-Millan, P., Rubio-Cosials, A., Arnan, C., Montoya, J., Jacobs, H.T., Bernado, P., Coll, M., Uson, I., Sola, M.

Revision History  

• Version 1.0: 2010-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations