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

(-) Description

Title :  STRUCTURE OF THE WILD-TYPE LARGE GAMMA SUBUNIT OF INITIATION FACTOR EIF2 FROM PYROCOCCUS ABYSSI COMPLEXED WITH GDP-MG2+
 
Authors :  E. Schmitt, S. Blanquet, Y. Mechulam
Date :  06 Dec 01  (Deposition) - 10 Apr 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Initiation Of Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Schmitt, S. Blanquet, Y. Mechulam
The Large Subunit Of Initiation Factor Aif2 Is A Close Structural Homologue Of Elongation Factors.
Embo J. V. 21 1821 2002
PubMed-ID: 11927566  |  Reference-DOI: 10.1093/EMBOJ/21.7.1821
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EIF2GAMMA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:60 , CYS A:63 , CYS A:72 , CYS A:75BINDING SITE FOR RESIDUE ZN A 411
2AC2SOFTWARETHR A:24 , GDP A:412 , HOH A:1090 , HOH A:1091 , HOH A:1096 , HOH A:1099BINDING SITE FOR RESIDUE MG A 413
3AC3SOFTWAREASP A:20 , HIS A:21 , GLY A:22 , LYS A:23 , THR A:24 , THR A:25 , ASN A:145 , LYS A:146 , GLU A:148 , LEU A:149 , SER A:180 , ALA A:181 , LEU A:182 , MG A:413 , HOH A:1002 , HOH A:1081 , HOH A:1088 , HOH A:1090 , HOH A:1091 , HOH A:1099BINDING SITE FOR RESIDUE GDP A 412

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KK3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Cys A:120 -Pro A:121
2Arg A:252 -Pro A:253

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KK3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KK3)

(-) Exons   (0, 0)

(no "Exon" information available for 1KK3)

(-) 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:398
 aligned with IF2G_PYRAB | Q9V1G0 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:405
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406     
           IF2G_PYRAB     7 SRQAEVNIGMVGHVDHGKTTLTKALTGVWTDTHSEELRRGITIKIGFADAEIRRCPNCGRYSTSPVCPYCGHETEFVRRVSFIDAPGHEALMTTMLAGASLMDGAILVIAANEPCPRPQTREHLMALQIIGQKNIIIAQNKIELVDKEKALENYRQIKEFIEGTVAENAPIIPISALHGANIDVLVKAIEDFIPTPKRDPNKPPKMLVLRSFDVNKPGTPPEKLVGGVLGGSIVQGKLKVGDEIEIRPGVPYEEHGRIKYEPITTEIVSLQAGGQFVEEAYPGGLVGVGTKLDPYLTKGDLMAGNVVGKPGKLPPVWDSLRLEVHLLERVVGTEQELKVEPIKRKEVLLLNVGTARTMGLVTGLGKDEIEVKLQIPVCAEPGDRVAISRQIGSRWRLIGYGIIKE 411
               SCOP domains d1kk3a3 A:6-200 Initiation fact  or eIF2 gamma subunit, N-terminal (G) domain                                                                                                                      d1kk3a1 A:201-321 Initi   ation factor eIF2 gamma subunit, domain II                                                     d1kk3a2 A:322-4  10 Initiation factor eIF2 gamma subunit                                  SCOP domains
               CATH domains 1kk3A01 A:6-203 P-loop containi  ng nucleotide triphosphate hydrolases                                                                                                                                1kk3A02 A:204-318 Tr   anslation factors                                                                           1kk3A03 A:319-410   Translation factors                                                      CATH domains
               Pfam domains --GTP_EFTU-1kk3A01 A:8-200                                                                                                                                                                         -----------------------   ----GTP_EFTU_D2-1kk3A02 A:231-313                                                      --------eIF2_C-1kk3A03   A:322-408                                                             -- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhh....--............eeeeeeeee......ee............eeeeeeeeee..hhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhh........eee.......hhhhhhhhhhhhh...........eeeeeeee......---......eeeeeeee..ee...eeeeeeeeeeee..eeeeeeeeeeeeeeee..ee..ee.....eeeee..hhhhhhhhh....eee.......eeeeeeeeeee.....--.............eeeeee..eeeeeeeeeee..eeeeeeeeeee.....eeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kk3 A   6 SRQAEVNIGMVGHVDHGKTTLTKALTGVWTD--SEELRRGITIKIGFADAEIRRCPNCGRYSTSPVCPYCGHETEFVRRVSFIDAPGHEALMTTMLAGASLMDGAILVIAANEPCPRPQTREHLMALQIIGQKNIIIAQNKIELVDKEKALENYRQIKEFIEGTVAENAPIIPISALHGANIDVLVKAIEDFIPTPKRDPNKPPKMLVLRSFDVNKPG---EKLVGGVLGGSIVQGKLKVGDEIEIRPGVPYEEHGRIKYEPITTEIVSLQAGGQFVEEAYPGGLVGVGTKLDPYLTKGDLMAGNVVGKPGKLPPVWDSLRLEVHLLERVV--EQELKVEPIKRKEVLLLNVGTARTMGLVTGLGKDEIEVKLQIPVCAEPGDRVAISRQIGSRWRLIGYGIIKE 410
                                    15        25        35|  |    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       | - |     235       245       255       265       275       285       295       305       315       325       335|  |   345       355       365       375       385       395       405     
                                                         36 39                                                                                                                                                                                     223 227                                                                                                          336  |                                                                       
                                                                                                                                                                                                                                                                                                                                                                       339
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: GTP_EFTU_D2] (39)
(-)
Clan: no clan defined [family: eIF2_C] (10)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IF2G_PYRAB | Q9V1G0)
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:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
    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:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
    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
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:252 - Pro A:253   [ RasMol ]  
    Cys A:120 - Pro A:121   [ 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 | Asym./Biol. Unit - sites 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
  1kk3
    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
  IF2G_PYRAB | Q9V1G0
    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
  IF2G_PYRAB | Q9V1G0
    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
        IF2G_PYRAB | Q9V1G0: 1kjz 1kk0 1kk1 1kk2

(-) Related Entries Specified in the PDB File

1kjz 1kk0 1kk1 1kk2