6HC3

TFAM bound to Site-X


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    6HB4, 6HC3

  • 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 this genome ...

    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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor A, mitochondrialA, D, G, J224Homo sapiensMutation(s): 0 
Gene Names: TFAMTCF6TCF6L2
UniProt & NIH Common Fund Data Resources
Find proteins for Q00059 (Homo sapiens)
Explore Q00059 
Go to UniProtKB:  Q00059
PHAROS:  Q00059
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
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
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
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
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.79α = 90
b = 145.136β = 130.83
c = 108.119γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-30
    Changes: Data collection, Derived calculations