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Title :   FITTING OF L11 PROTEIN AND ELONGATION FACTOR G (DOMAIN G' AND V) IN THE CRYO-EM MAP OF E. COLI 70S RIBOSOME BOUND WITH EF-G AND GMPPCP, A NONHYDROLYSABLE GTP ANALOG

Authors :   R. K. Agrawal, J. Linde, J. Segupta, K. H. Nierhaus, J. Frank

Date :   07 Aug 01 (Deposition) - 07 Sep 01 (Release) - 24 Feb 09 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   NOT APPLICABLE

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   L11, Ef-G, Cryo-Em, 70S E. Coli Ribosome, Gtp State (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. K. Agrawal, J. Linde, J. Sengupta, K. H. Nierhaus, J. Frank
Localization Of L11 Protein On The Ribosome And Elucidation Of Its Involvement In Ef-G-Dependent Translocation.
J. Mol. Biol. V. 311 777 2001
PubMed-ID: 11518530 | Reference-DOI: 10.1006/JMBI.2001.4907
(for further references see the PDB file header)

Compounds

Molecule 1 - 50S RIBOSOMAL PROTEIN L11
	Chains	:	A
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	L11 FROM E. COLI 70S RIBOSOME MODELED BY CRYSTAL STRUCTURE OF L11 FROM THERMATOGOMA MARITIMA

Molecule 2 - ELONGATION FACTOR G
	Chains	:	B
	Fragment	:	PART OF DOMAIN G'
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	EF-G FROM E. COLI 70S RIBOSOME MODELED BY CRYSTAL STRUCTURE OF EF-G FROM THERMUS THERMOPHILUS
	Synonym	:	EF-G; TRANSLATION ELONGATION FACTOR EF-G

Molecule 3 - ELONGATION FACTOR G
	Chains	:	C
	Fragment	:	DOMAIN V
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	EF-G FROM E. COLI 70S RIBOSOME MODELED BY CRYSTAL STRUCTURE OF EF-G FROM THERMUS THERMOPHILUS
	Synonym	:	EF-G; TRANSLATION ELONGATION FACTOR EF-G

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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:133
 aligned with RL11_THEMA | P29395 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:133
                                    17        27        37        47        57        67        77        87        97       107       117       127       137   
           RL11_THEMA     8 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV 140
               SCOP domains d1jqsa_ A: 70S ribosome functional complex                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L11   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jqs A   1 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:32
 aligned with EFG_THETH | P13551 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:32
                                   229       239       249  
            EFG_THETH   220 AADFDENIMLKYLEGEEPTEEELVAAIRKGTI 251
               SCOP domains d1jqsb_ B:                       SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                 1jqs B 220 AADFDENIMLKYLEGEEPTEEELVAAIRKGTI 251
                                   229       239       249

Chain C from PDB  Type:PROTEIN  Length:68
 aligned with EFG_THETH | P13551 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:68
                                   615       625       635       645       655       665        
            EFG_THETH   606 MRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFF 673
               SCOP domains d1jqsc_ C: 70S ribosome functional complex                           SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 1jqs C 606 MRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFF 673
                                   615       625       635       645       655       665

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 (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 17)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RL11_THEMA | P29395)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0070180	large ribosomal subunit rRNA binding	Interacting selectively and non-covalently with the large ribosomal subunit RNA (LSU rRNA), a constituent of the large ribosomal subunit. In S. cerevisiae, this is the 25S rRNA.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0000027	ribosomal large subunit assembly	The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.
	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.
cellular component
	GO:0022625	cytosolic large ribosomal subunit	The large subunit of a ribosome located in the cytosol.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain B,C (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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