Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A C-TERMINAL SEGMENT OF THE ALPHA SUBUNIT OF AIF2 FROM PYROCOCCUS ABYSSI
 
Authors :  L. Yatime, E. Schmitt, S. Blanquet, Y. Mechulam
Date :  28 Feb 05  (Deposition) - 28 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A
Keywords :  Helical Domain, Alpha-Beta Domain, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Yatime, E. Schmitt, S. Blanquet, Y. Mechulam
Structure-Function Relationships Of The Intact Aif2Alpha Subunit From The Archaeon Pyrococcus Abyssi
Biochemistry V. 44 8749 2005
PubMed-ID: 15952781  |  Reference-DOI: 10.1021/BI050373I
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE TRANSLATION INITIATION FACTOR 2 ALPHA SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DOMAINS 2 AND 3(RESIDUES 89-275)
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292
    Synonym: EIF-2-ALPHA, AIF2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1YZ7)

(-) Sites  (0, 0)

(no "Site" information available for 1YZ7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YZ7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:221 -Pro A:222

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YZ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YZ7)

(-) Exons   (0, 0)

(no "Exon" information available for 1YZ7)

(-) Sequences/Alignments

Asymmetric/Biological 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:176
 aligned with IF2A_PYRAB | Q9V0E4 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:176
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
           IF2A_PYRAB    91 KAKLQEFKRAQKAENLLKLAAEKLGKDFETAWREVWVPLEEEWGEVYAAFEDAAKDGIDVLKGHVPDEWLPVLKEIIDNYVEVPTVTIDAEFEITVPKPNGVEIIKEALIRARDRANKEKDVEVKFTYLGAPRYRIDITAPDYYKAEEVLESIAEEILRVIKEAGGEATLLRKEKR 266
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------EIF_2_alpha-1yz7A01 A:120-233                                                                                     --------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh....eeeeeeeeee....hhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh..eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yz7 A  91 KAKLQEFKRAQKAENLLKLAAEKLGKDFETAWREVWVPLEEEWGEVYAAFEDAAKDGIDVLKGHVPDEWLPVLKEIIDNYVEVPTVTIDAEFEITVPKPNGVEIIKEALIRARDRANKEKDVEVKFTYLGAPRYRIDITAPDYYKAEEVLESIAEEILRVIKEAGGEATLLRKEKR 266
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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 1YZ7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YZ7)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: EIF_2_alpha] (5)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IF2A_PYRAB | Q9V0E4)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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

Asymmetric/Biological Unit
  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 1yz7)
 
  Sites
(no "Sites" information available for 1yz7)
 
  Cis Peptide Bonds
    Ala A:221 - Pro A:222   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  1yz7
    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
  IF2A_PYRAB | Q9V0E4
    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
  IF2A_PYRAB | Q9V0E4
    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
        IF2A_PYRAB | Q9V0E4: 1yz6

(-) Related Entries Specified in the PDB File

1yz6 ENTIRE CHAIN OF THE SAME PROTEIN