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(-) Description

Title :  DISTINCT STRUCTURAL FEATURES OF TFAM DRIVE MITOCHONDRIAL DNA PACKAGING VERSUS TRANSCRIPTIONAL ACTIVATION
 
Authors :  H. B. Ngo, G. A. Lovely, R. Phillips, D. C. Chan
Date :  19 Nov 13  (Deposition) - 22 Jan 14  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Biol. Unit 3:  G,I,J  (1x)
Biol. Unit 4:  H,K,L  (1x)
Keywords :  Hmg, Dna Bending, Tfb2M, Mtrnap, Bru Substitution To Hsp1, T19, Transcription Regulator-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. B. Ngo, G. A. Lovely, R. Phillips, D. C. Chan
Distinct Structural Features Of Tfam Drive Mitochondrial Dn Packaging Versus Transcriptional Activation.
Nat Commun V. 5 3077 2014
PubMed-ID: 24435062  |  Reference-DOI: 10.1038/NCOMMS4077

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR A, MITOCHONDRIAL
    Chains: A, B, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A+
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 43-237
    Gene: TCF6, TCF6L2, TFAM
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TFAM, MTTFA, MITOCHONDRIAL TRANSCRIPTION FACTOR 1, MTTF1, TRANSCRIPTION FACTOR 6, TCF-6, TRANSCRIPTION FACTOR 6-LIKE 2
 
Molecule 2 - 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP *(BRU)P*TP*GP*G)-3'
    Chains: C, E, I, K
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: HEAVY STRAND PROMOTER 1 (HSP1)
 
Molecule 3 - 5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP *CP*CP*AP*A)-3'
    Chains: D, F, J, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: HEAVY STRAND PROMOTER 1 (HSP1)

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): A CD        
Biological Unit 2 (1x):  B  EF      
Biological Unit 3 (1x):       G IJ  
Biological Unit 4 (1x):        H  KL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1BRU4Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BRU1Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BRU1Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1BRU1Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1BRU1Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4NOD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NOD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NOD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NOD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NOD)

(-) Exons   (0, 0)

(no "Exon" information available for 4NOD)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nod A  44 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRR 233
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nod B  44 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRR 233
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233


Chain C from PDB  Type:DNA  Length:22
                                                      
                 4nod C   1 TTGGGGTATGGGGCTTGGuTGG  22
                                    10        20  
                                             19-BRU


Chain D from PDB  Type:DNA  Length:22
                                                      
                 4nod D   1 CCAACCAAGCCCCATACCCCAA  22
                                    10        20  


Chain E from PDB  Type:DNA  Length:22
                                                      
                 4nod E   1 TTGGGGTATGGGGCTTGGuTGG  22
                                    10        20  
                                             19-BRU


Chain F from PDB  Type:DNA  Length:22
                                                      
                 4nod F   1 CCAACCAAGCCCCATACCCCAA  22
                                    10        20  


Chain G from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nod G  44 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRR 233
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233


Chain H from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nod H  44 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRR 233
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233


Chain I from PDB  Type:DNA  Length:22
                                                      
                 4nod I   1 TTGGGGTATGGGGCTTGGuTGG  22
                                    10        20  
                                             19-BRU


Chain J from PDB  Type:DNA  Length:22
                                                      
                 4nod J   1 CCAACCAAGCCCCATACCCCAA  22
                                    10        20  


Chain K from PDB  Type:DNA  Length:22
                                                      
                 4nod K   1 TTGGGGTATGGGGCTTGGuTGG  22
                                    10        20  
                                             19-BRU


Chain L from PDB  Type:DNA  Length:22
                                                      
                 4nod L   1 CCAACCAAGCCCCATACCCCAA  22
                                    10        20
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4NOD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NOD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NOD)

(-) Gene Ontology  (26, 26)

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        TFAM_HUMAN | Q00059: 3fgh 3tmm 3tq6 4nnu

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