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(-) Description

Title :  THE STRUCTURES OF AIF2GAMMA SUBUNIT FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS IN THE GDP-BOUND FORM.
 
Authors :  O. S. Nikonov, E. A. Stolboushkina, A. D. Nikulin, D. Hasenohrl, U. Blaesi, D. J. Manstein, R. V. Fedorov, M. B. Garber, S. V Nikonov
Date :  21 Apr 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Aif2, Initiation Factor 2 Gamma Subunit, Initiation Of The Translation, Nucleotide Binding, Gdpnp, Gdp, Pyrophosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Nikonov, E. Stolboushkina, A. Nikulin, D. Hasenohrl, U. Blasi, D. J. Manstein, R. Fedorov, M. Garber, S. Nikonov
New Insights Into The Interactions Of The Translation Initiation Factor 2 From Archaea With Guanine Nucleotides And Initiator Trna.
J. Mol. Biol. V. 373 328 2007
PubMed-ID: 17825838  |  Reference-DOI: 10.1016/J.JMB.2007.07.048
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR 2 GAMMA SUBUNIT
    Chains: A, B
    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
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: EIF-2-GAMMA, AIF2- GAMMA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3PPV6Ligand/IonPYROPHOSPHATE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3PPV3Ligand/IonPYROPHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GNP-1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3PPV3Ligand/IonPYROPHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:18 , ASP A:19 , GLY A:21 , LYS A:22 , THR A:23 , THR A:24 , GLY A:96 , ASN A:149 , LYS A:150 , ASP A:152 , VAL A:153 , SER A:184 , ALA A:185 , LEU A:186 , PPV A:419BINDING SITE FOR RESIDUE GDP A 416
2AC2SOFTWAREASP B:19 , GLY B:21 , LYS B:22 , THR B:23 , THR B:24 , GLY B:96 , ASN B:149 , LYS B:150 , ASP B:152 , VAL B:153 , SER B:184 , ALA B:185 , LEU B:186 , PPV B:418BINDING SITE FOR RESIDUE GDP B 416
3AC3SOFTWAREGLU A:40 , ARG A:43 , GLY A:44 , MET A:45 , ASP A:222 , VAL A:223 , ASN A:224 , LYS A:225 , SER A:278 , ILE A:279 , ARG A:280 , ALA A:296 , GLY A:298 , LYS A:307 , HOH A:421BINDING SITE FOR RESIDUE GNP A 417
4AC4SOFTWAREGLY B:258 , LEU B:259 , ARG B:260 , TYR B:269 , ASN B:310 , LEU B:311 , HOH B:434 , HOH B:461BINDING SITE FOR RESIDUE PPV B 417
5AC5SOFTWAREGLY A:258 , LEU A:259 , ARG A:260 , ASN A:310 , ARG A:384BINDING SITE FOR RESIDUE PPV A 418
6AC6SOFTWARELEU A:186 , HIS A:187 , GDP A:416BINDING SITE FOR RESIDUE PPV A 419
7AC7SOFTWARELEU B:186 , HIS B:187 , PRO B:324 , GDP B:416 , HOH B:473BINDING SITE FOR RESIDUE PPV B 418
8AC8SOFTWAREGLN A:229 , PHE A:230 , THR B:274 , LYS B:275 , TYR B:300 , HOH B:456BINDING SITE FOR RESIDUE PPV B 419
9AC9SOFTWARETHR A:274 , LYS A:275 , TYR A:300 , HOH A:459 , HOH A:468 , THR B:228 , GLN B:229 , PHE B:230 , HOH B:444BINDING SITE FOR RESIDUE PPV A 420

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:59 -A:74
2A:62 -A:77
3B:59 -B:74
4B:62 -B:77

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Lys A:64 -Pro A:65
2Phe A:124 -Pro A:125
3Leu A:256 -Pro A:257
4Lys B:64 -Pro B:65
5Phe B:124 -Pro B:125
6Leu B:256 -Pro B:257

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PMD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PMD)

(-) Exons   (0, 0)

(no "Exon" information available for 2PMD)

(-) Sequences/Alignments

Asymmetric 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:414
 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 d2pmda3 A:2-206 Initiation factor eIF2 gamma subunit, N-terminal (G) domain                                                                                                                                  d2pmda1 A:207-320 Initiation factor eIF2 gamma subunit, domain II                                                 d2pmda2 A:321-415 Initiation factor eIF2 gamma subunit                                          SCOP domains
               CATH domains 2pmdA01 A:2-207 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                          2pmdA02 A:208-322 Translation factors                                                                              2pmdA03 A:323-415 Translation factors                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeee....hhhhhhhhhhh..................eeeeeeeee.........ee....hhhhh.....eeeeeeeeee........hhhhhh.....eeeeeee......hhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhh....hhhhhh.eee.......hhhhhhhhhhhhh...........eeeeeeee.......hhhhh...eeeeeeee..ee...eeeeeeeeeeee..eeeeeeeeee..eeee..eee.ee.....eeee...hhhhh........eeee......eeeeeeeeeee....................eeeeee..eeeeeeeeee...eeeeeeeeeee......eeeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pmd A   2 AWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSEELKRGMTIKLGYAETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGWGLVEI 415
                                    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    


Chain B from PDB  Type:PROTEIN  Length:414
 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 d2pmdb3 B:2-206 Initiation factor eIF2 gamma subunit, N-terminal (G) domain                                                                                                                                  d2pmdb1 B:207-320 Initiation factor eIF2 gamma subunit, domain II                                                 d2pmdb2 B:321-415 Initiation factor eIF2 gamma subunit                                          SCOP domains
               CATH domains 2pmdB01 B:2-207 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                          2pmdB02 B:208-322 Translation factors                                                                              2pmdB03 B:323-415 Translation factors                                                         CATH domains
           Pfam domains (1) -----GTP_EFTU-2pmdB01 B:7-204                                                                                                                                                                              ------------------------------GTP_EFTU_D2-2pmdB03 B:235-308                                             -----------------eIF2_C-2pmdB05 B:326-413                                                                -- Pfam domains (1)
           Pfam domains (2) -----GTP_EFTU-2pmdB02 B:7-204                                                                                                                                                                              ------------------------------GTP_EFTU_D2-2pmdB04 B:235-308                                             -----------------eIF2_C-2pmdB06 B:326-413                                                                -- Pfam domains (2)
         Sec.struct. author .........eeeeee....hhhhhhhhhh.......hhhhhh......eeeeeeeee.........ee..............eeeeeeeeee..........hhhhhh...eeeeeee......hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhh..hhhhhh.eee.......hhhhhhhhhhhhh...........eeeeeeee.......hhhhh...eeeeeeee..ee...eeeeeeeeee......eeeeeeee..eeee..eee.ee.....eeee...hhhhhh.......eeee......eeeeeeeeeee....................eeeeee..eeeeeeeeee...eeeeeeeeeee......eeeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pmd B   2 AWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSEELKRGMTIKLGYAETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGWGLVEI 415
                                    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
   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, 6)

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

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (3, 6)

Asymmetric 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 Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IF2G_SULSO | Q980A5: 2aho 2plf 2qmu 2qn6 3cw2 3i1f 3pen 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

2aho AIF2GAMMA SUBUNIT FROM THE SAME ARCHAEON IN THE GDP-BOUND FORM.