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Asym./Biol. Unit (Jmol Viewer)

Title :   COORDINATES OF THE N-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11,C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L7/L12 AND A PORTION OF THE G' DOMAIN OF ELONGATION FACTOR G, AS FITTED INTO CRYO-EM MAP OF AN ESCHERICHIA COLI 70S*EF-G*GDP*FUSIDIC ACID COMPLEX

Authors :   P. P. Datta, M. R. Sharma, L. Qi, J. Frank, R. K. Agrawal

Date :   19 Oct 05 (Deposition) - 20 Dec 05 (Release) - 24 Feb 09 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   11.20

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

Keywords :   Components Involved In Interaction Between Ef-G And L7/L12 Stalk Base Of The Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. P. Datta, M. R. Sharma, L. Qi, J. Frank, R. K. Agrawal
Interaction Of The G' Domain Of Elongation Factor G And The C-Terminal Domain Of Ribosomal Protein L7/L12 During Translocation As Revealed By Cryo-Em.
Mol. Cell V. 20 723 2005
PubMed-ID: 16337596 | Reference-DOI: 10.1016/J.MOLCEL.2005.10.028
(for further references see the PDB file header)

Molecule 1 - 50S RIBOSOMAL PROTEIN L11
	Chains	:	A
	Fragment	:	N-TERMINAL DOMAIN
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

Molecule 2 - 50S RIBOSOMAL PROTEIN L7/L12
	Chains	:	B
	Fragment	:	C-TERMINAL DOMAIN
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	L8

Molecule 3 - ELONGATION FACTOR G
	Chains	:	C
	Fragment	:	A PORTION OF G' DOMAIN'
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	EF-G

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2BCW)

(no "Site" information available for 2BCW)

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

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

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

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

(no "Exon" information available for 2BCW)

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
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Chain A from PDB  Type:PROTEIN  Length:65
 aligned with RL11_THEMA | P29395 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:65
                                    17        27        37        47        57        67     
           RL11_THEMA     8 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKT  72
               SCOP domains d2bcwa1 A:8-70 Ribosomal protein L11, N-terminal domain        -- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 2bcw A   8 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKT  72
                                    17        27        37        47        57        67

Chain B from PDB  Type:PROTEIN  Length:68
 aligned with RL7_ECOLI | P0A7K2 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:68
                                    63        73        83        93       103       113        
            RL7_ECOLI    54 EFDVILKAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAGAEVEVK 121
               SCOP domains d2bcwb1 B:53-120 Ribosomal protein L7/12, C-terminal domain          SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2bcw B  53 EFDVILKAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAGAEVEVK 120
                                    62        72        82        92       102       112

Chain C from PDB  Type:PROTEIN  Length:58
 aligned with EFG_THETH | P13551 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:58
                                   209       219       229       239       249        
            EFG_THETH   200 PIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITP 257
               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
                 2bcw C 200 PIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITP 257
                                   209       219       229       239       249

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	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 '\|'

(no "CATH Domain" information available for 2BCW)

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

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 (RL7_ECOLI | P0A7K2)

molecular function
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of 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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0022625	cytosolic large ribosomal subunit	The large subunit of a ribosome located in the cytosol.
	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.
	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 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.

Asymmetric/Biological Unit
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1ctf	C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L7/L12 FROM ESCHERICHIA COLI
1elo	A PORTION OF G' DOMAIN OF EF-G FROM THERMUS THERMOPHILUS
1mms	N-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11 FROM THERMOTOGA MARITIMA

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