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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PED208 TRAM-SBMA COMPLEX
 
Authors :  J. J. W. Wong, J. Lu, R. A. Edwards, L. S. Frost, J. N. Mark Glover
Date :  27 Aug 10  (Deposition) - 25 May 11  (Release) - 07 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.87
Chains :  Asym. Unit :  A,B,C,D,P
Biol. Unit 1:  A,B,C,D,P  (2x)
Keywords :  Dna Binding Protein, Dna Protein-Dna Complex, Tetramer, Cooperative Binding, Unwinding Of Dna, Kinking Of Dna, Plasmid Conjugation, Bacterial Conjugation, Ribbon-Helix-Helix, 4-Helix Bundle, Transcriptional Repressor, Dna, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Wong, J. Lu, R. A. Edwards, L. S. Frost, J. N. Glover
Structural Basis Of Cooperative Dna Recognition By The Plasmid Conjugation Factor, Tram.
Nucleic Acids Res. V. 39 6775 2011
PubMed-ID: 21565799  |  Reference-DOI: 10.1093/NAR/GKR296

(-) Compounds

Molecule 1 - PROTEIN TRAM
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: TRAM
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - SBMA
    Chains: P
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED OLIGO
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDP
Biological Unit 1 (2x): ABCDP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3ON0)

(-) Sites  (0, 0)

(no "Site" information available for 3ON0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ON0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly C:58 -Phe C:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ON0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ON0)

(-) Exons   (0, 0)

(no "Exon" information available for 3ON0)

(-) 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:121
 aligned with TRAM8_ECOLX | P33788 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:125
                                    11        21        31        41        51        61        71        81        91       101       111       121     
          TRAM8_ECOLX     2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQQEKREGGFNQMEYNKLMLENVSRVRAMCTEILKMSVLNQESIASGNFDYAVIKPAIDKFAREQVSIFFPDDEDDQ 126
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.----.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3on0 A   2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQQEK----FNQMEYNKLMLENVSRVRAMCTEILKMSVLNQESIASGNFDYAVIKPAIDKFAREQVSIFFPDDEDDQ 126
                                    11        21        31        41        51  |    |61        71        81        91       101       111       121     
                                                                               54   59                                                                   


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with TRAM8_ECOLX | P33788 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:118
                                    11        21        31        41        51        61        71        81        91       101       111        
          TRAM8_ECOLX     2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQQEKREGGFNQMEYNKLMLENVSRVRAMCTEILKMSVLNQESIASGNFDYAVIKPAIDKFAREQVSIFF 119
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3on0 B   2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQQEKREGGFNQMEYNKLMLENVSRVRAMCTEILKMSVLNQESIASGNFDYAVIKPAIDKFAREQVSIFF 119
                                    11        21        31        41        51        61        71        81        91       101       111        


Chain C from PDB  Type:PROTEIN  Length:118
 aligned with TRAM8_ECOLX | P33788 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:118
                                    11        21        31        41        51        61        71        81        91       101       111        
          TRAM8_ECOLX     2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQQEKREGGFNQMEYNKLMLENVSRVRAMCTEILKMSVLNQESIASGNFDYAVIKPAIDKFAREQVSIFF 119
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3on0 C   2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQQEKREGGFNQMEYNKLMLENVSRVRAMCTEILKMSVLNQESIASGNFDYAVIKPAIDKFAREQVSIFF 119
                                    11        21        31        41        51        61        71        81        91       101       111        


Chain D from PDB  Type:PROTEIN  Length:107
 aligned with TRAM8_ECOLX | P33788 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:118
                                    11        21        31        41        51        61        71        81        91       101       111        
          TRAM8_ECOLX     2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQQEKREGGFNQMEYNKLMLENVSRVRAMCTEILKMSVLNQESIASGNFDYAVIKPAIDKFAREQVSIFF 119
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Tra_M-3on0D01 D:2-119                                                                                                  Pfam domains (1)
           Pfam domains (2) Tra_M-3on0D02 D:2-119                                                                                                  Pfam domains (2)
           Pfam domains (3) Tra_M-3on0D03 D:2-119                                                                                                  Pfam domains (3)
           Pfam domains (4) Tra_M-3on0D04 D:2-119                                                                                                  Pfam domains (4)
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh-----------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3on0 D   2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRV-----------FNQMEYNKLMLENVSRVRAMCTEILKMSVLNQESIASGNFDYAVIKPAIDKFAREQVSIFF 119
                                    11        21        31        41     |   -       |61        71        81        91       101       111        
                                                                        47          59                                                            


Chain P from PDB  Type:DNA  Length:24
                                                        
                 3on0 P   1 AGATTCGAATCTAGATTCGAATCT  24
                                    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 3ON0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ON0)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Tra_M] (2)
(-)
Family: Tra_M (2)
(-)
Escherichia coli (2)
1aTra_M-3on0D01D:2-119
1bTra_M-3on0D02D:2-119
1cTra_M-3on0D03D:2-119
1dTra_M-3on0D04D:2-119

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TRAM8_ECOLX | P33788)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  Sites
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  Cis Peptide Bonds
    Gly C:58 - Phe C:59   [ RasMol ]  
 
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TRAM8_ECOLX | P33788: 3omy

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