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 ARCHAEAL INITIATION FACTOR AIF2GAMMA SUBUNIT DELTA 37-47 FROM SULFOLOBUS SOLFATARICUS IN THE GDP-BOUND FORM.
 
Authors :  V. I. Arkhipova, A. M. Lazopulo, S. M. Lazopulo, M. B. Garber, O. S. Nikon S. V. Nikonov, A. G. Gabdoulkhakov
Date :  27 Oct 10  (Deposition) - 04 May 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Rna, Met, Archaeal Proteins, Binding Sites, Prokaryotic Init Factor- 2, Guanosine Diphosphate, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. I. Arkhipova, A. M. Lazopulo, S. M. Lazopulo, M. B. Garber, O. S. Nikonov, S. V. Nikonov, A. G. Gabdoulkhakov
Structure Of Archaeal Initiation Factor Aif2Gamma Subunit From Sulfolobus Solfataricus In The Gdp-Bound Form.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR 2 SUBUNIT GAMMA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11D
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EIF2G, SSO0412
    Mutation: YES
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: AIF2-GAMMA, EIF-2-GAMMA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG5Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:19 , HIS A:20 , GLY A:21 , LYS A:22 , THR A:23 , THR A:24 , HOH A:41 , ASN A:149 , LYS A:150 , ASP A:152 , SER A:184 , ALA A:185 , LEU A:186 , MG A:419 , HOH A:530 , HOH A:574 , HOH A:580 , HOH A:622 , HOH A:626 , HOH A:638 , HOH A:652 , HOH A:660BINDING SITE FOR RESIDUE GDP A 416
2AC2SOFTWAREPHE A:221 , VAL A:223 , LYS A:234 , SER A:278 , ARG A:280 , GLY A:282 , ALA A:296 , GLY A:298 , HOH A:661 , HOH A:668BINDING SITE FOR RESIDUE 5GP A 1
3AC3SOFTWARETHR A:54 , THR A:70 , HOH A:591 , HOH A:594 , HOH A:603 , HOH A:611BINDING SITE FOR RESIDUE MG A 417
4AC4SOFTWAREVAL A:151 , VAL A:154 , TRP A:327 , ASN A:328 , HOH A:582 , HOH A:596BINDING SITE FOR RESIDUE MG A 418
5AC5SOFTWARETHR A:23 , LYS A:48 , GDP A:416 , HOH A:574 , HOH A:589BINDING SITE FOR RESIDUE MG A 419
6AC6SOFTWAREGLU A:66 , TYR A:68 , ASP A:192 , HOH A:581 , HOH A:617BINDING SITE FOR RESIDUE MG A 420
7AC7SOFTWAREMET A:111 , HOH A:588 , HOH A:601 , HOH A:610 , HOH A:615 , HOH A:616BINDING SITE FOR RESIDUE MG A 421

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:59 -A:74
2A:62 -A:77

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Lys A:48 -Leu A:49
2Lys A:64 -Pro A:65
3Phe A:124 -Pro A:125
4Leu A:256 -Pro A:257
5Lys A:263 -Gln A:264

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PEN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PEN)

(-) Exons   (0, 0)

(no "Exon" information available for 3PEN)

(-) 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:403
 aligned with IF2G_SULSO | Q980A5 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:414
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411    
           IF2G_SULSO     2 AWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSEELKRGMTIKLGYAETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGWGLVEI 415
               SCOP domains d3pena1 A:2-206 automated matches                                                                                                                                                                            d3pena2 A:207-320 automated matches                                                                               d3pena3 A:321-415 automated matches                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----GTP_EFTU-3penA01 A:7-204                                                                                                                                                                              ------------------------------GTP_EFTU_D2-3penA02 A:235-308                                             -----------------eIF2_C-3penA03 A:326-413                                                                -- Pfam domains
         Sec.struct. author .........eeeee.....hhhhhhhhhhh.....-----------..eeeeeeeee.........ee....hhhhh.....eeeeeeeeee...hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhh........eee.......hhhhhhhhhhhhh...........eeeeeeee.......hhhhh...eeeeeeee..ee...eeeeeeeeee......eeeeeeee..eeee..eee.ee.....eeee...hhhhhhhhh....eeee......eeeeeeeeeee....................eeeeee..eeeeeeeeee...eeeeeeeeeee.....eeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pen A   2 AWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSK-----------KLGYAETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGWGLVEI 415
                                    11        21        31    |    -      | 51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411    
                                                             36          48
   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  (0, 0)

(no "CATH Domain" information available for 3PEN)

(-) 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  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IF2G_SULSO | Q980A5)
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:0001731    formation of translation preinitiation complex    The joining of the small ribosomal subunit, ternary complex, and mRNA.
    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.
cellular component
    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

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
    5GP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:256 - Pro A:257   [ RasMol ]  
    Lys A:263 - Gln A:264   [ RasMol ]  
    Lys A:48 - Leu A:49   [ RasMol ]  
    Lys A:64 - Pro A:65   [ RasMol ]  
    Phe A:124 - Pro A:125   [ 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
  3pen
    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_SULSO | Q980A5
    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_SULSO | Q980A5
    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_SULSO | Q980A5: 2aho 2plf 2pmd 2qmu 2qn6 3cw2 3i1f 3qsy 3sjz 3v11 4m0l 4m2l 4m4s 4m53 4nbs 4qfm 4qhy 4rcy 4rcz 4rd0 4rd1 4rd2 4rd3 4rd4 4rd6 4rjl 5dsz 5jb3 5jbh

(-) Related Entries Specified in the PDB File

2plf AIF2GAMMA IN THE NUCLEOTIDE-FREE FORM
2pmd AIF2GAMMA IN COMPLEX WITH GDP AND GPP(NH)P