3TMM

TFAM imposes a U-turn on mitochondrial DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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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: https://doi.org/10.1038/nsmb.2159
  • Primary Citation of Related Structures:  
    3TMM

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor A, mitochondrial238Homo sapiensMutation(s): 0 
Gene Names: TCF6TCF6L2TFAM
UniProt & NIH Common Fund Data Resources
Find proteins for Q00059 (Homo sapiens)
Explore Q00059 
Go to UniProtKB:  Q00059
PHAROS:  Q00059
GTEx:  ENSG00000108064 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00059
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (28-MER)28N/A
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (28-MER)28N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.438α = 90
b = 81.911β = 90
c = 161.254γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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