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 :  ARCHAEAL INITIATION FACTOR-1A, AIF-1A
 
Authors :  D. W. Hoffman, W. Li
Date :  20 Aug 01  (Deposition) - 05 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Beta Barrel, Translation Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Li, D. W. Hoffman
Structure And Dynamics Of Translation Initiation Factor Aif-1A From The Archaeon Methanococcus Jannaschii Determined By Nmr Spectroscopy
Protein Sci. V. 10 2426 2001
PubMed-ID: 11714910  |  Reference-DOI: 10.1110/PS.PS.18201
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE TRANSLATION INITIATION FACTOR 1A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificMETHANOCALDOCOCCUS JANNASCHII
    Organism Taxid2190
    SynonymEIF-1A

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1JT8)

(-) Sites  (0, 0)

(no "Site" information available for 1JT8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JT8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JT8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JT8)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S1_IF1_TYPEPS50832 S1 domain IF1 type profile.IF1A_METJA10-85  1A:10-85
2IF1APS01262 Eukaryotic initiation factor 1A signature.IF1A_METJA29-51  1A:29-51

(-) Exons   (0, 0)

(no "Exon" information available for 1JT8)

(-) 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:102
 aligned with IF1A_METJA | Q57887 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:102
                                    10        20        30        40        50        60        70        80        90       100  
           IF1A_METJA     1 MAEQQQEQQIRVRIPRKEENEILGIIEQMLGASRVRVRCLDGKTRLGRIPGRLKNRIWVREGDVVIVKPWEVQGDQKCDIIWRYTKTQVEWLKRKGYLDELL 102
               SCOP domains d1jt8a_ A: Archaeal initiation factor-1a, aIF1a                                                        SCOP domains
               CATH domains 1jt8A00 A:1-102 Nucleic acid-binding proteins                                                          CATH domains
               Pfam domains -----------------eIF-1a-1jt8A01 A:18-83                                            ------------------- Pfam domains
         Sec.struct. author .....................eeeeee......eeeeeee..eeeeee.hhhhhhhhh....eeeee........eeeeeeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------S1_IF1_TYPE  PDB: A:10-85 UniProt: 10-85                                    ----------------- PROSITE (1)
                PROSITE (2) ----------------------------IF1A  PDB: A:29-51     --------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1jt8 A   1 MAEQQQEQQIRVRIPRKEENEILGIIEQMLGASRVRVRCLDGKTRLGRIPGRLKNRIWVREGDVVIVKPWEVQGDQKCDIIWRYTKTQVEWLKRKGYLDELL 102
                                    10        20        30        40        50        60        70        80        90       100  

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: OB (224)

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A   (IF1A_METJA | Q57887)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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.

 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 1jt8)
 
  Sites
(no "Sites" information available for 1jt8)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1jt8)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1jt8
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  IF1A_METJA | Q57887
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  IF1A_METJA | Q57887
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1JT8)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1JT8)