3TMM

TFAM imposes a U-turn on mitochondrial DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5001 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA.

Ngo, H.B.Kaiser, J.T.Chan, D.C.

(2011) Nat.Struct.Mol.Biol. 18: 1290-1296

  • DOI: 10.1038/nsmb.2159

  • PubMed Abstract: 
  • Tfam (transcription factor A, mitochondrial), a DNA-binding protein with tandem high-mobility group (HMG)-box domains, has a central role in the expression, maintenance and organization of the mitochondrial genome. It activates transcription from mit ...

    Tfam (transcription factor A, mitochondrial), a DNA-binding protein with tandem high-mobility group (HMG)-box domains, has a central role in the expression, maintenance and organization of the mitochondrial genome. It activates transcription from mitochondrial promoters and organizes the mitochondrial genome into nucleoids. Using X-ray crystallography, we show that human Tfam forces promoter DNA to undergo a U-turn, reversing the direction of the DNA helix. Each HMG-box domain wedges into the DNA minor groove to generate two kinks on one face of the DNA. On the opposite face, a positively charged α-helix serves as a platform to facilitate DNA bending. The structural principles underlying DNA bending converge with those of the unrelated HU family proteins, which have analogous architectural roles in organizing bacterial nucleoids. The functional importance of this extreme DNA bending is promoter specific and seems to be related to the orientation of Tfam on the promoters.


    Organizational Affiliation

    Division of Biology, California Institute of Technology, Pasadena, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription factor A, mitochondrial
A
238Homo sapiensMutation(s): 0 
Gene Names: TFAM (TCF6, TCF6L2)
Find proteins for Q00059 (Homo sapiens)
Go to Gene View: TFAM
Go to UniProtKB:  Q00059
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (28-MER)B28N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (28-MER)C28N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5001 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 68.438α = 90.00
b = 81.911β = 90.00
c = 161.254γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXmodel building
XDSdata reduction
SCALAdata scaling
Blu-Icedata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2011-11-16
    Type: Database references