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(-) Description

Title :  TRANSLATIONAL ELONGATION FACTOR G COMPLEXED WITH GDP
 
Authors :  J. Czworkowski, J. Wang, T. A. Steitz, P. B. Moore
Date :  23 Sep 98  (Deposition) - 30 Sep 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Elongation Factor, Translocase, Ribosome, Elongation, Translation, Protein Synt Factor, Gtpase, Gtp Binding, Guanosine Nucleotide Binding, , Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Czworkowski, J. Wang, T. A. Steitz, P. B. Moore
The Crystal Structure Of Elongation Factor G Complexed With Gdp, At 2. 7 A Resolution.
Embo J. V. 13 3661 1994
PubMed-ID: 8070396
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (ELONGATION FACTOR G)
    Chains: A
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: EF-G
 
Molecule 2 - PROTEIN (ELONGATION FACTOR G DOMAIN 3)
    Chains: B
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: EF-G

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 53)

Asymmetric/Biological Unit (2, 53)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2UNK52Mod. Amino Acid

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:22 , ALA A:23 , GLY A:24 , LYS A:25 , THR A:26 , THR A:27 , ASN A:137 , LYS A:138 , ASP A:140 , SER A:262 , ALA A:263 , LEU A:264 , HOH A:920BINDING SITE FOR RESIDUE GDP A 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EFG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EFG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.EFG_THET853-68  1A:67-68
EFG_THETH53-68  1A:67-68

(-) Exons   (0, 0)

(no "Exon" information available for 2EFG)

(-) 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:582
 aligned with EFG_THET8 | Q5SHN5 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:683
                                    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       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686   
            EFG_THET8     7 YDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIK 689
               SCOP domains d2efga2 A:7-282 Elongation factor                            G (EF-G), N-terminal (G) domain                                                                                                                                                                                        d2efga1 A:283-401 Elongation factor G (EF-G), domain II                                                                                                                                          d2efga3 A:476-599 Elongation factor G (EF-G), domain IV                                                                     d2efga4 A:600-689 Elongation factor G (EF-G)                                               SCOP domains
               CATH domains 2efgA01 A:7-286 P-loop containing                            nucleotide triphosphate hydrolases                                                                                                                                                                                         ----------------2efgA02 A:303-400 Translation factors                                                             -                                                                          --------2efgA03 A:484-602  [code=3.30.230.10, no name defined]                                                                 2efgA04 A:603-685  [code=3.30.70.240, no name defined]                             ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.....hhhhhhhhhhhhh..---------------------------..eeeeee..eeeeee........hhhhhhhhhh..eeeeeee......hhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhh...eee.eeee..hhh..eeee....eeeee.......eeee...hhhhhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhh....eeeee........hhhhhhhhhh..........eee.......eee........eeee.eee.......eeeeeeee......eeee......eeee.eeeeee..eeeee.......eeeee.........eee...........--------------------------------------------------------------------------........eee....eeeeeeee........eeeeeeee........eeeee...........hhhhhhhhhhhhh...........eeeeeeeee.......hhhhhhhhhhhhhhhhh....eeeeeeeeeeeeee...hhhhhhhhhhh............eeee..eeehhhh...hhhhhhh.....eeeeeeeeeee..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2efg A   7 YDLKRLRNIGIAAHIDAGKTTTTERILYYTGRI---------------------------AAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDNAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILES--------------------------------------------------------------------------VGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIK 689
                                    16        26        36  |      -         -         -|       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    |    -         -         -         -         -         -         -       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686   
                                                           39                          67                                                                                                                                                                                                                                                                                                                                           401                                                                        476                                                                                                                                                                                                                     


Chain A from PDB  Type:PROTEIN  Length:582
 aligned with EFG_THETH | P13551 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:683
                                    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       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686   
            EFG_THETH     7 YDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIK 689
               SCOP domains d2efga2 A:7-282 Elongation factor                            G (EF-G), N-terminal (G) domain                                                                                                                                                                                        d2efga1 A:283-401 Elongation factor G (EF-G), domain II                                                                                                                                          d2efga3 A:476-599 Elongation factor G (EF-G), domain IV                                                                     d2efga4 A:600-689 Elongation factor G (EF-G)                                               SCOP domains
               CATH domains 2efgA01 A:7-286 P-loop containing                            nucleotide triphosphate hydrolases                                                                                                                                                                                         ----------------2efgA02 A:303-400 Translation factors                                                             -                                                                          --------2efgA03 A:484-602  [code=3.30.230.10, no name defined]                                                                 2efgA04 A:603-685  [code=3.30.70.240, no name defined]                             ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.....hhhhhhhhhhhhh..---------------------------..eeeeee..eeeeee........hhhhhhhhhh..eeeeeee......hhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhh...eee.eeee..hhh..eeee....eeeee.......eeee...hhhhhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhh....eeeee........hhhhhhhhhh..........eee.......eee........eeee.eee.......eeeeeeee......eeee......eeee.eeeeee..eeeee.......eeeee.........eee...........--------------------------------------------------------------------------........eee....eeeeeeee........eeeeeeee........eeeee...........hhhhhhhhhhhhh...........eeeeeeeee.......hhhhhhhhhhhhhhhhh....eeeeeeeeeeeeee...hhhhhhhhhhh............eeee..eeehhhh...hhhhhhh.....eeeeeeeeeee..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2efg A   7 YDLKRLRNIGIAAHIDAGKTTTTERILYYTGRI---------------------------AAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDNAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILES--------------------------------------------------------------------------VGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIK 689
                                    16        26        36  |      -         -         -|       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    |    -         -         -         -         -         -         -       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686   
                                                           39                          67                                                                                                                                                                                                                                                                                                                                           401                                                                        476                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:52
                                                                                    
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh......................hhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 2efg B 704 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 791
                            |||||||713|||||||724|||||||758|||||||769|||||||789||
                          704-UNK||713-UNK||723-UNK||756-UNK||766-UNK||785-UNK||
                           705-UNK||714-UNK||724-UNK||757-UNK||767-UNK||786-UNK|
                            706-UNK||715-UNK||725-UNK||758-UNK||768-UNK||787-UNK
                             707-UNK| 717-UNK| 726-UNK| 760-UNK| 769-UNK| 788-UNK
                              708-UNK  718-UNK  729-UNK  761-UNK  770-UNK  789-UNK
                               709-UNK  719-UNK  730-UNK  762-UNK  771-UNK  790-UNK
                                710-UNK  720-UNK  731-UNK  763-UNK  772-UNK  791-UNK
                                 711-UNK  721-UNK  732-UNK  764-UNK  773-UNK    
                                  712-UNK  722-UNK  755-UNK  765-UNK  774-UNK
   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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EFG)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (EFG_THET8 | Q5SHN5)
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.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

Chain A   (EFG_THETH | P13551)
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.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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  2efg
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  EFG_THET8 | Q5SHN5
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  EFG_THETH | P13551
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 Related Entries

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

UniProtKB/Swiss-Prot
        EFG_THET8 | Q5SHN5: 1dar 1efg 1elo 1zn0 4v5f 4v5m 4v5n 4v8u 4v90 4v9h 4wpo 4wqf 4wqu 4wqy 5hau
        EFG_THETH | P13551: 1efg 1fnm 1ip8 1ipm 1ipo 1ipr 1jqm 1jqs 1ktv 1pn6 2bcw 2bm0 2bm1 2bv3 2j7k 2om7 3izp 4m1k 4myt 4myu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2EFG)