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 C1-SUBDOMAIN OF BACILLUS STEAROTHERMOPHILUS TRANSLATION INITIATION FACTOR IF2
 
Authors :  H. Wienk, S. Tomaselli, C. Bernard, R. Spurio, D. Picone, C. O. Gualerzi, R. Boelens
Date :  01 Apr 05  (Deposition) - 30 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Protein Synthesis Translation Intiation If2 Fmet-Trna Nmr Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wienk, S. Tomaselli, C. Bernard, R. Spurio, D. Picone, C. O. Gualerzi, R. Boelens
Solution Structure Of The C1-Subdomain Of Bacillus Stearothermophilus Translation Initiation Factor If2
Protein Sci. V. 14 2461 2005
PubMed-ID: 16081655  |  Reference-DOI: 10.1110/PS.051531305
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR IF-2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEV
    Expression System Strain: JM109/PCI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: BST IF2-C1 SUBDOMAIN
    Gene: INFB
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1Z9B)

(-) Sites  (0, 0)

(no "Site" information available for 1Z9B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z9B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z9B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z9B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z9B)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z9B)

(-) 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:135
 aligned with IF2_GEOSE | P04766 from UniProtKB/Swiss-Prot  Length:741

    Alignment length:137
                                   508       518       528       538       548       558       568       578       588       598       608       618       628       
            IF2_GEOSE   499 DEKKARQIGEARAQRQLQEQRSVKTRVSLDDLFEQIKQGEMKELNLIVKADVQGSVEALVAALQKIDVEGVRVKIIHAAVGAITESDISLATASNAIVIGFNVRPDANAKRAAESEKVDIRLHRIIYNVIEEIEAAM 635
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------IF-2-1z9bA01 A:25-133                                                                                        -- Pfam domains
         Sec.struct. author ..............--..........................eeeeeeee.hhhhhhhhhhhhh.......eeeeeeeee...hhhhhhhhhhhh.eeee.......hhhhhhhh.....ee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z9b A   1 NEFELGTRGSSRVD--LQEQRSVKTRVSLDDLFEQIKQGEMKELNLIVKADVQGSVEALVAALQKIDVEGVRVKIIHAAVGAITESDISLATASNAIVIGFNVRPDANAKRAAESEKVDIRLHRIIYNVIEEIEAAM 135
                                    10   |  | 18        28        38        48        58        68        78        88        98       108       118       128       
                                        14 15
   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 1Z9B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z9B)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: IF-2] (2)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (IF2_GEOSE | P04766)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0003743    translation initiation factor activity    Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006413    translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

 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 1z9b)
 
  Sites
(no "Sites" information available for 1z9b)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1z9b)
 

(-) 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
  1z9b
    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
  IF2_GEOSE | P04766
    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
  IF2_GEOSE | P04766
    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
        IF2_GEOSE | P04766: 1d1n 2lkc 2lkd 2nbg

(-) Related Entries Specified in the PDB File

4697 1H, 15N AND 13C CHEMICAL SHIFTS FOR IF2-C2
6577 1H, 15N AND 13C CHEMICAL SHIFTS, PEAK ASSIGNMENTS, RELAXATION DATA AND SQUARED ORDER PARAMETERS FOR IF2-C1
1d1n SOLUTION STRUCTURE OF THE C2-SUBDOMAIN OF BACILLUS STEAROTHERMOPHILUS IF2 (SAME PROTEIN)