Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS RNA POLYMERASE BINDING PROTEIN A (RBPA) AND ITS INTERACTIONS WITH SIGMA FACTORS
 
Authors :  A. Bortoluzzi, F. W. Muskett, L. C. Waters, P. W. Addis, B. Rieck, T. Mund S. Schleier, F. Forti, D. Ghisotti, M. D. Carr, H. M. O'Hare
Date :  11 Feb 13  (Deposition) - 17 Apr 13  (Release) - 07 Aug 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (35x)
NMR Structure *:  A  (1x)
Keywords :  Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bortoluzzi, F. W. Muskett, L. C. Waters, P. W. Addis, B. Rieck, T. Munder, S. Schleier, F. Forti, D. Ghisotti, M. D. Carr, H. M. O'Hare
Mycobacterium Tuberculosis Rna Polymerase-Binding Protein A (Rbpa) And Its Interactions With Sigma Factors.
J. Biol. Chem. V. 288 14438 2013
PubMed-ID: 23548911  |  Reference-DOI: 10.1074/JBC.M113.459883

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-43.1A(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MB2076, MT2110, RV2050
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: ATCC BAA-935 / AF2122/97

 Structural Features

(-) Chains, Units

  1
NMR Structure (35x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2M4V)

(-) Sites  (0, 0)

(no "Site" information available for 2M4V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M4V)

(-) Cis Peptide Bonds  (27, 82)

NMR Structure
No.ModelResidues
11, 28Gly A:9 -Ser A:10
21, 26Gly A:13 -Ala A:14
31, 11, 15, 16, 19, 20, 21, 23, 24, 26, 33Pro A:78 -Pro A:79
42, 17, 25, 26, 28, 33Ser A:1 -Met A:2
52, 3, 13, 14, 17, 21, 24, 26, 29, 34Lys A:77 -Pro A:78
63, 9, 28Arg A:11 -Leu A:12
73, 6, 30, 32Pro A:79 -Arg A:80
84, 12Ser A:10 -Arg A:11
94Asp A:69 -Leu A:70
105Glu A:67 -Gly A:68
116, 10His A:23 -Asp A:24
126, 14, 15, 16, 19, 29Leu A:70 -Pro A:71
1310, 17, 32, 34Ala A:3 -Asp A:4
1411, 17, 30Asp A:4 -Arg A:5
1512, 19, 28Met A:2 -Ala A:3
1613, 14, 20, 30, 32Val A:15 -Ser A:16
1716, 31Tyr A:17 -Glu A:18
1818, 33, 35Asp A:20 -Arg A:21
1921, 31Leu A:7 -Arg A:8
2023Thr A:19 -Asp A:20
2124Ser A:16 -Tyr A:17
2224, 35Val A:76 -Lys A:77
2325, 29Arg A:21 -Asn A:22
2426Leu A:12 -Gly A:13
2530Pro A:71 -Glu A:72
2632Arg A:8 -Gly A:9
2735Asn A:22 -His A:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M4V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2M4V)

(-) Exons   (0, 0)

(no "Exon" information available for 2M4V)

(-) Sequences/Alignments

NMR Structure
   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:80
 aligned with O53492_MYCTU | O53492 from UniProtKB/TrEMBL  Length:111

    Alignment length:80
                             1                                                                              
                             |       9        19        29        39        49        59        69        79
          O53492_MYCTU    - -MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR 79
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhh...eeeeeee.....eeeeeee.......eee.....eeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                  2m4v A  1 SMADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR 80
                                    10        20        30        40        50        60        70        80


Chain A from PDB  Type:PROTEIN  Length:80
 aligned with RBPA_MYCTU | P9WHJ5 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:80
                             1                                                                              
                             |       9        19        29        39        49        59        69        79
            RBPA_MYCTU    - -MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR 79
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhh...eeeeeee.....eeeeeee.......eee.....eeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                  2m4v A  1 SMADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPR 80
                                    10        20        30        40        50        60        70        80
   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 2M4V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M4V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M4V)

(-) Gene Ontology  (6, 8)

NMR Structure(hide GO term definitions)
Chain A   (O53492_MYCTU | O53492)
molecular function
    GO:0001000    bacterial-type RNA polymerase core enzyme binding    Interacting selectively and non-covalently with the bacterial-type RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one omega subunit.
biological process
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.

Chain A   (RBPA_MYCTU | P9WHJ5)
molecular function
    GO:0001000    bacterial-type RNA polymerase core enzyme binding    Interacting selectively and non-covalently with the bacterial-type RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one omega subunit.
biological process
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2m4v)
 
  Sites
(no "Sites" information available for 2m4v)
 
  Cis Peptide Bonds
    Ala A:3 - Asp A:4   [ RasMol ]  
    Arg A:11 - Leu A:12   [ RasMol ]  
    Arg A:21 - Asn A:22   [ RasMol ]  
    Arg A:8 - Gly A:9   [ RasMol ]  
    Asn A:22 - His A:23   [ RasMol ]  
    Asp A:20 - Arg A:21   [ RasMol ]  
    Asp A:4 - Arg A:5   [ RasMol ]  
    Asp A:69 - Leu A:70   [ RasMol ]  
    Glu A:67 - Gly A:68   [ RasMol ]  
    Gly A:13 - Ala A:14   [ RasMol ]  
    Gly A:9 - Ser A:10   [ RasMol ]  
    His A:23 - Asp A:24   [ RasMol ]  
    Leu A:12 - Gly A:13   [ RasMol ]  
    Leu A:7 - Arg A:8   [ RasMol ]  
    Leu A:70 - Pro A:71   [ RasMol ]  
    Lys A:77 - Pro A:78   [ RasMol ]  
    Met A:2 - Ala A:3   [ RasMol ]  
    Pro A:71 - Glu A:72   [ RasMol ]  
    Pro A:78 - Pro A:79   [ RasMol ]  
    Pro A:79 - Arg A:80   [ RasMol ]  
    Ser A:1 - Met A:2   [ RasMol ]  
    Ser A:10 - Arg A:11   [ RasMol ]  
    Ser A:16 - Tyr A:17   [ RasMol ]  
    Thr A:19 - Asp A:20   [ RasMol ]  
    Tyr A:17 - Glu A:18   [ RasMol ]  
    Val A:15 - Ser A:16   [ RasMol ]  
    Val A:76 - Lys A:77   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2m4v
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  O53492_MYCTU | O53492
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  RBPA_MYCTU | P9WHJ5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  O53492_MYCTU | O53492
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RBPA_MYCTU | P9WHJ5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RBPA_MYCTU | P9WHJ5: 2m6p 4x8k

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2M4V)