6HC3

TFAM bound to Site-X


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region.

Cuppari, A.Fernandez-Millan, P.Battistini, F.Tarres-Sole, A.Lyonnais, S.Iruela, G.Ruiz-Lopez, E.Enciso, Y.Rubio-Cosials, A.Prohens, R.Pons, M.Alfonso, C.Toth, K.Rivas, G.Orozco, M.Sola, M.

(2019) Nucleic Acids Res. 47: 6519-6537

  • DOI: 10.1093/nar/gkz406
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human mitochondrial DNA (h-mtDNA) codes for 13 subunits of the oxidative phosphorylation pathway, the essential route that produces ATP. H-mtDNA transcription and replication depends on the transcription factor TFAM, which also maintains and compacts ...

    Human mitochondrial DNA (h-mtDNA) codes for 13 subunits of the oxidative phosphorylation pathway, the essential route that produces ATP. H-mtDNA transcription and replication depends on the transcription factor TFAM, which also maintains and compacts this genome. It is well-established that TFAM activates the mtDNA promoters LSP and HSP1 at the mtDNA control region where DNA regulatory elements cluster. Previous studies identified still uncharacterized, additional binding sites at the control region downstream from and slightly similar to LSP, namely sequences X and Y (Site-X and Site-Y) (Fisher et al., Cell 50, pp 247-258, 1987). Here, we explore TFAM binding at these two sites and compare them to LSP by multiple experimental and in silico methods. Our results show that TFAM binding is strongly modulated by the sequence-dependent properties of Site-X, Site-Y and LSP. The high binding versatility of Site-Y or the considerable stiffness of Site-X tune TFAM interactions. In addition, we show that increase in TFAM/DNA complex concentration induces multimerization, which at a very high concentration triggers disruption of preformed complexes. Therefore, our results suggest that mtDNA sequences induce non-uniform TFAM binding and, consequently, direct an uneven distribution of TFAM aggregation sites during the essential process of mtDNA compaction.


    Organizational Affiliation

    Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain.,Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain.,Unitat de Polimorfisme i Calorimetria, Centres Científics i Tecnològics, University of Barcelona, 08028 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,BioNMR Laboratory, Inorganic and Organic Chemistry Department, Universitat de Barcelona, 08028 Barcelona, Spain.,Deutsches Krebsforschungszentrum, Division Biophysics of Macromolecules, Heidelberg, Germany.,Structural MitoLab, Structural Biology Department, Maria de Maeztu Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), 08028 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription factor A, mitochondrial
A, D, G, J
224Homo 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/RNA (5'-D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)-3')B,E,H,K22Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)-3')C,F,I,L22Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download SDF File 
Download CCD File 
A, D, G
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A, D, G, J
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 164.790α = 90.00
b = 145.136β = 130.83
c = 108.119γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2015-70645-R

Revision History 

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Data collection, Database references