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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ELONGATION FACTOR G COMPLEXED WITH GDP, AT 2.7 ANGSTROMS RESOLUTION
 
Authors :  J. Czworkowski, J. Wang, T. A. Steitz, P. B. Moore
Date :  17 Oct 94  (Deposition) - 14 Feb 95  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Elongation Factor (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 - ELONGATION FACTOR G
    Chains: A
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Strain: HB8
 
Molecule 2 - ELONGATION FACTOR G
    Chains: B
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Strain: HB8
 
Molecule 3 - ELONGATION FACTOR G
    Chains: C
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Strain: HB8

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 65)

Asymmetric/Biological Unit (2, 65)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2UNK64Mod. Amino Acid

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:22 , GLY A:24 , LYS A:25 , LYS A:138 , SER A:262BINDING SITE FOR RESIDUE GDP A 692

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EFG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:66-68
EFG_THETH53-68  1A:66-68

(-) Exons   (0, 0)

(no "Exon" information available for 1EFG)

(-) 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:592
 aligned with EFG_THET8 | Q5SHN5 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:689
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680         
            EFG_THET8     1 MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIK 689
               SCOP domains d1efga2 A:1-282 Elongation factor G (EF-G                        ), N-terminal (G) domain                                                                                                                                                                                                 d1efga1 A:283-403 Elongation factor G (EF-G), domain II                                                                                                                                           d1efga3 A:477-599 Elongation factor G (EF-G), domain IV                                                                    d1efga4 A:600-689 Elongation factor G (EF-G)                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................................------------------------..................................................................................................................................................................................................................................................................................................................................................-------------------------------------------------------------------------..................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1efg A   1 MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHK------------------------TAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDNAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIE-------------------------------------------------------------------------GKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIK 689
                                    10        20        30        40|        -         -     |  70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400  |      -         -         -         -         -         -         -      |480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680         
                                                                   41                       66                                                                                                                                                                                                                                                                                                                                              403                                                                       477                                                                                                                                                                                                                    


Chain A from PDB  Type:PROTEIN  Length:592
 aligned with EFG_THETH | P13551 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:689
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680         
            EFG_THETH     1 MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIK 689
               SCOP domains d1efga2 A:1-282 Elongation factor G (EF-G                        ), N-terminal (G) domain                                                                                                                                                                                                 d1efga1 A:283-403 Elongation factor G (EF-G), domain II                                                                                                                                           d1efga3 A:477-599 Elongation factor G (EF-G), domain IV                                                                    d1efga4 A:600-689 Elongation factor G (EF-G)                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................................------------------------..................................................................................................................................................................................................................................................................................................................................................-------------------------------------------------------------------------..................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------G_TR_1          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1efg A   1 MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHK------------------------TAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDNAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIE-------------------------------------------------------------------------GKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIK 689
                                    10        20        30        40|        -         -     |  70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400  |      -         -         -         -         -         -         -      |480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680         
                                                                   41                       66                                                                                                                                                                                                                                                                                                                                              403                                                                       477                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:36
                                                                    
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author .................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 1efg B 700 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 735
                            |||||||709|||||||719|||||||729||||||
                          700-UNK||709-UNK||718-UNK||727-UNK||||
                           701-UNK||710-UNK||719-UNK||728-UNK|||
                            702-UNK||711-UNK||720-UNK||729-UNK||
                             703-UNK| 712-UNK| 721-UNK| 730-UNK|
                              704-UNK  713-UNK  722-UNK  731-UNK
                               705-UNK  714-UNK  723-UNK  732-UNK
                                706-UNK  715-UNK  724-UNK  733-UNK
                                 707-UNK  716-UNK  725-UNK  734-UNK
                                  708-UNK  717-UNK  726-UNK  735-UNK


Chain C from PDB  Type:PROTEIN  Length:28
                                                            
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author ............................ Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 1efg C 800 xxxxxxxxxxxxxxxxxxxxxxxxxxxx 827
                            |||||||809|||||||819||||||||
                            ||||||808-UNK||817-UNK||826-UNK
                          800-UNK||809-UNK||818-UNK||827-UNK
                           801-UNK||810-UNK||819-UNK||  
                            802-UNK| 811-UNK| 820-UNK|  
                             803-UNK  812-UNK  821-UNK  
                              804-UNK  813-UNK  822-UNK 
                               805-UNK  814-UNK  823-UNK
                                806-UNK  815-UNK  824-UNK
                                 807-UNK  816-UNK  825-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  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EFG)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
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.

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.

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1EFG)