4NOD Transcription Regulator Dna date Nov 19, 2013
title Distinct Structural Features Of Tfam Drive Mitochondrial Dna Versus Transcriptional Activation
authors H.B.Ngo, G.A.Lovely, R.Phillips, D.C.Chan
compound source
Molecule: Transcription Factor A, Mitochondrial
Chain: A, B, G, H
Fragment: Unp Residues 43-237
Synonym: Tfam, Mttfa, Mitochondrial Transcription Factor 1, Transcription Factor 6, Tcf-6, Transcription Factor 6-Like
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tcf6, Tcf6l2, Tfam
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a+

Molecule: 5'-D(Tptpgpgpgpgptpaptpgpgpgpgpcpt (Bru)Ptpgpg)-3';
Chain: C, E, I, K
Engineered: Yes
Other_details: Heavy Strand Promoter 1 (Hsp1)

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'-D(Cpcpapapcpcpapapgpcpcpcpcpapt Cpcpapa)-3';
Chain: D, F, J, L
Engineered: Yes
Other_details: Heavy Strand Promoter 1 (Hsp1)

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.221 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.372 82.490 104.222 79.86 85.48 84.53
method X-Ray Diffractionresolution 2.90 Å
ligand BRU enzyme
Primary referenceDistinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation., Ngo HB, Lovely GA, Phillips R, Chan DC, Nat Commun. 2014 Jan 17;5:3077. doi: 10.1038/ncomms4077. PMID:24435062
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (430 Kb) [Save to disk]
  • Biological Unit Coordinates (4nod.pdb1.gz) 108 Kb
  • Biological Unit Coordinates (4nod.pdb2.gz) 107 Kb
  • Biological Unit Coordinates (4nod.pdb3.gz) 106 Kb
  • Biological Unit Coordinates (4nod.pdb4.gz) 106 Kb
  • LPC: Ligand-Protein Contacts for 4NOD
  • CSU: Contacts of Structural Units for 4NOD
  • Structure Factors (1847 Kb)
  • Retrieve 4NOD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NOD from S2C, [Save to disk]
  • Re-refined 4nod structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NOD in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4NOD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4NOD, from MSDmotif at EBI
  • Fold representative 4nod from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nod_E] [4nod_G] [4nod_A] [4nod_D] [4nod_C] [4nod_K] [4nod] [4nod_B] [4nod_I] [4nod_F] [4nod_L] [4nod_H] [4nod_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4NOD: [HMG ] by SMART
  • Other resources with information on 4NOD
  • Community annotation for 4NOD at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science