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 :  SOLUTION STRUCTURE OF THE N-UTILISATION SUBSTANCE G (NUSG) C-TERMINAL (NGC) DOMAIN FROM THERMUS THERMOPHILUS
 
Authors :  P. Reay, K. Yamasaki, T. Terada, S. Kuramitsu, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 Feb 03  (Deposition) - 06 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (31x)
Keywords :  Transcription Elongation, Termination, Antitermination, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Reay, K. Yamasaki, T. Terada, S. Kuramitsu, M. Shirouzu, S. Yokoyama
Structural And Sequence Comparisons Arising From The Solution Structure Of The Transcription Elongation Factor Nusg From Thermus Thermophilus
Proteins V. 56 40 2004
PubMed-ID: 15162485  |  Reference-DOI: 10.1002/PROT.20054
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION ANTITERMINATION PROTEIN NUSG
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL (NGC) DOMAIN
    Gene: NUSG
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: N-UTILISATION SUBSTANCE G

 Structural Features

(-) Chains, Units

  
NMR Structure (31x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1NZ9)

(-) Sites  (0, 0)

(no "Site" information available for 1NZ9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NZ9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NZ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NZ9)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUSGPS01014 Transcription termination factor nusG signature.NUSG_THET8167-176  1A:167-176

(-) Exons   (0, 0)

(no "Exon" information available for 1NZ9)

(-) 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:58
 aligned with NUSG_THET8 | P35872 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:58
                                   136       146       156       166       176        
           NUSG_THET8   127 AQVAFREGDQVRVVSGPFADFTGTVTEINPERGKVKVMVTIFGRETPVELDFSQVVKA 184
               SCOP domains d1nz9a_ A:                                                 SCOP domains
               CATH domains 1nz9A00 A:127-184  [code=2.30.30.30, no name defined]      CATH domains
               Pfam domains ------KOW-1nz9A01 A:133-168               ---------------- Pfam domains
         Sec.struct. author .........eeee........eeeeeeee....eeeeeee....eeeeee.hhheee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------NUSG      -------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 1nz9 A 127 AQVAFREGDQVRVVSGPFADFTGTVTEINPERGKVKVMVTIFGRETPVELDFSQVVKA 184
                                   136       146       156       166       176
   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  (1, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: KOW (56)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (NUSG_THET8 | P35872)
biological process
    GO:0006354    DNA-templated transcription, elongation    The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.
    GO:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    GO:0032784    regulation of DNA-templated transcription, elongation    Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0031564    transcription antitermination    Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
    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 1nz9)
 
  Sites
(no "Sites" information available for 1nz9)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nz9)
 

(-) 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
  1nz9
    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
  NUSG_THET8 | P35872
    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
  NUSG_THET8 | P35872
    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
        NUSG_THET8 | P35872: 1nz8

(-) Related Entries Specified in the PDB File

1nz8 N-TERMINAL (NGN) DOMAIN RELATED ID: TTK003000790.2 RELATED DB: TARGETDB