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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   COMPLEX OF ELONGATING ESCHERICHIA COLI 70S RIBOSOME AND EF4(LEPA)-GMPPNP

Authors :   S. R. Connell, M. Topf, Y. Qin, D. N. Wilson, T. Mielke, P. Fucini, K. H. Ni C. M. T. Spahn

Date :   10 Jun 08 (Deposition) - 19 Aug 08 (Release) - 16 Apr 14 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   10.90

Chains :   Asym./Biol. Unit : A,B,C,D,E,F,G,H,I,J,K

Keywords :   Ribosome, Translation, Lepa, Ef4, Gtp-Binding, Membrane, Nucleotide- Binding, Antibiotic Resistance, Ribonucleoprotein, Ribosomal Protein, Rna-Binding, Rrna-Binding, Trna-Binding, Methylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. R. Connell, M. Topf, Y. Qin, D. N. Wilson, T. Mielke, P. Fucini, K. H. Nierhaus, C. M. T. Spahn
A New Trna Intermediate Revealed On The Ribosome During Ef4-Mediated Back-Translocation
Nat. Struct. Mol. Biol. V. 15 910 2008
PubMed-ID: 19172743 | Reference-DOI: 10.1038/NSMB.1469

Molecule 1 - A/L-TRNA
	Chains	:	A
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - P-TRNA
	Chains	:	B
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 3 - 30S RNA HELIX 8
	Chains	:	E
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 4 - 30S RNA HELIX 14
	Chains	:	F
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 5 - 50S RNA HELIX 42-44
	Chains	:	G
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 6 - 50S RNA HELIX 95
	Chains	:	I
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 7 - 50S RNA HELIX 71
	Chains	:	J
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 8 - 50S RNA HELIX 92
	Chains	:	K
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 9 - GTP-BINDING PROTEIN LEPA
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	EF4
	Gene	:	LEPA, B2569, JW2553
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

Molecule 10 - 30S RIBOSOMAL PROTEIN S12
	Chains	:	D
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

Molecule 11 - 50S RIBOSOMAL PROTEIN L11
	Chains	:	H
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		1	2	3	4	5	6	7	8	9	10	11
Asymmetric/Biological Unit	:	A	B	C	D	E	F	G	H	I	J	K

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (11, 15)

No.	Name	Count	Type	Full Name
1	1MA	1	Mod. Nucleotide	6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
2	2MG	1	Mod. Nucleotide	2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
3	5MC	2	Mod. Nucleotide	5-METHYLCYTIDINE-5'-MONOPHOSPHATE
4	5MU	2	Mod. Nucleotide	5-METHYLURIDINE 5'-MONOPHOSPHATE
5	7MG	1	Mod. Nucleotide	7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
6	H2U	2	Mod. Nucleotide	5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
7	M2G	1	Mod. Nucleotide	N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
8	OMC	1	Mod. Nucleotide	O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
9	OMG	1	Mod. Nucleotide	O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
10	PSU	2	Mod. Nucleotide	PSEUDOURIDINE-5'-MONOPHOSPHATE
11	YG	1	Mod. Residue	WYBUTOSINE

(no "Site" information available for 3DEG)

(no "SS Bond" information available for 3DEG)

Asymmetric/Biological Unit

No.	Residues
1	Gly C:30	-	Leu C:31
2	Thr C:241	-	Pro C:242

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_RS12_ECOLI_001 *	K	43	R	RS12_ECOLI	---	---	D	K	42	R
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	LEPA_ECOLI	42-57	1	C:42-57
2	RIBOSOMAL_S12	PS00055	Ribosomal protein S12 signature.	RS12_ECOLI	43-50	1	D:42-49
3	RIBOSOMAL_L11	PS00359	Ribosomal protein L11 signature.	RL11_ECOLI	127-142	1	H:126-141

(no "Exon" information available for 3DEG)

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:RNA  Length:76
                                                                                                             
                3deg A    1 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAGgUCcUGUGuuCGaUCCACAGAAUUCGCACCA   76
                                    10     || 20     |  30 | |  | 40     |  50   ||  |60        70      
                                    10-2MG ||       26-M2G | |  | ||     |  |    55-PSU                 
                                          16-H2U          32-OMC| ||     |  |    |  58-1MA              
                                           17-H2U           34-OMG||     |  |    |                      
                                                               37-YG     |  |    |                      
                                                                 39-PSU  |  |    |                      
                                                                  40-5MC |  |    |                      
                                                                        46-7MG   |                      
                                                                           49-5MC|                      
                                                                                54-5MU

Chain B from PDB  Type:RNA  Length:77
                                                                                                              
                3deg B    1 CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGuUCAAAUCCGGCCCCCGCAACCA   76
                                    10       |19        29        39        49    |   59        69       
                                           17A                                   54-5MU

Chain C from PDB  Type:PROTEIN  Length:545
 aligned with LEPA_ECOLI | P60785 from UniProtKB/Swiss-Prot  Length:599

    Alignment length:545
                                    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     
          LEPA_ECOLI      1 MKNIRNFSIIAHIDHGKSTLSDRIIQICGGLSDREMEAQVLDSMDLERERGITIKAQSVTLDYKASDGETYQLNFIDTPGHVDFSYEVSRSLAACEGALLVVDAGQGVEAQTLANCYTAMEMDLEVVPVLNKIDLPAADPERVAEEIEDIVGIDATDAVRCSAKTGVGVQDVLERLVRDIPPPEGDPEGPLQALIIDSWFDNYLGVVSLIRIKNGTLRKGDKVKVMSTGQTYNADRLGIFTPKQVDRTELKCGEVGWLVCAIKDIHGAPVGDTLTLARNPAEKALPGFKKVKPQVYAGLFPVSSDDYEAFRDALGKLSLNDASLFYEPESSSALGFGFRCGFLGLLHMEIIQERLEREYDLDLITTAPTVVYEVETTSREVIYVDSPSKLPAVNNIYELREPIAECHMLLPQAYLGNVITLCVEKRGVQTNMVYHGNQVALTYEIPMAEVVLDFFDRLKSTSRGYASLDYNFKRFQASDMVRVDVLINGERVDALALITHRDNSQNRGRELVEKMKDLIPRQQFDIAIQAAIGTHIIARSTVKQL  545
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......hhhhhhhhhhh...............hhhhhhhh.......eeeeee.....eeeeeeee......hhhhhhhhhh...eeeeeee......hhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhh........ee.......hhhhhhhhhhhhh...........eeeeeeeeee...eeeeeeeeee..ee...eeee.....eee..eeeee...eee..ee....eeeee.............eeee..................eeeeeee.hhhhhhhhhhhhhhhhh.....eeeeeee...eeeeeeee.hhhhhhhhhhhhhhh....eee......eeeee....eeee.hhhhh.hhh.eeeeeeeeeeeeeeee..hhhhhhhhhhhh..eeeeeeee..eeeeeeeeehhhhhh.hhhhhhhhh....eeeeeeeeeee..eeeeeeee....hhhhheeee..hhhhhhhhhhhhhhhhh......eeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------G_TR_1          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3deg C    1 MKNIRNFSIIAHIDHGKSTLSDRIIQICGGLSDREMEAQVLDSMDLERERGITIKAQSVTLDYKASDGETYQLNFIDTPGHVDFSYEVSRSLAACEGALLVVDAGQGVEAQTLANCYTAMEMDLEVVPVLNKIDLPAADPERVAEEIEDIVGIDATDAVRCSAKTGVGVQDVLERLVRDIPPPEGDPEGPLQALIIDSWFDNYLGVVSLIRIKNGTLRKGDKVKVMSTGQTYNADRLGIFTPKQVDRTELKCGEVGWLVCAIKDIHGAPVGDTLTLARNPAEKALPGFKKVKPQVYAGLFPVSSDDYEAFRDALGKLSLNDASLFYEPESSSALGFGFRCGFLGLLHMEIIQERLEREYDLDLITTAPTVVYEVETTSREVIYVDSPSKLPAVNNIYELREPIAECHMLLPQAYLGNVITLCVEKRGVQTNMVYHGNQVALTYEIPMAEVVLDFFDRLKSTSRGYASLDYNFKRFQASDMVRVDVLINGERVDALALITHRDNSQNRGRELVEKMKDLIPRQQFDIAIQAAIGTHIIARSTVKQL  545
                                    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

Chain D from PDB  Type:PROTEIN  Length:123
 aligned with RS12_ECOLI | P0A7S3 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:123
                                    11        21        31        41        51        61        71        81        91       101       111       121   
          RS12_ECOLI      2 ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA  124
               SCOP domains d3degd1 D:1-123 Ribosomal protein S12                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.........................eee.............eeee.......eeee...............eee..........eee........................... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------R--------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------RIBOSOMA-------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                3deg D    1 ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA  123
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain E from PDB  Type:RNA  Length:16
                                                 
                3deg E  153 CUACUGGAAACGGUAG  168
                                   162

Chain F from PDB  Type:RNA  Length:12
                                             
                3deg F  339 CUCCUACGGGAG  350
                                   348

Chain G from PDB  Type:RNA  Length:70
                                                                                                       
                3deg G 1043 CCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCGAG 1112
                                  1052      1062      1072      1082      1092      1102      1112

Chain H from PDB  Type:PROTEIN  Length:141
 aligned with RL11_ECOLI | P0A7J7 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
          RL11_ECOLI      2 AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVED  142
               SCOP domains d3degh2 H:1-72 Ribosomal protein L11, N-terminal domain                 d3degh1 H:73-141 Ribosomal protein L11, C-terminal domain             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...........hhhhhh...hhhhhhhhhhhhhhhhh....eeeeeee.....eeeee....hhhhhhhhhh.............eeeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L11    PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3deg H    1 AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVED  141
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain I from PDB  Type:RNA  Length:29
                                                              
                3deg I 2646 CUGCUCCUAGUACGAGAGGACCGGAGUGG 2674
                                  2655      2665

Chain J from PDB  Type:RNA  Length:18
                                                   
                3deg J 1944 UGUCGGGUAAGUUCCGAC 1961
                                  1953

Chain K from PDB  Type:RNA  Length:15
                                                
                3deg K 2547 AUGGCUGUUCGCCAU 2561
                                  2556

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 '\|'

(no "CATH Domain" information available for 3DEG)

(no "Pfam Domain" information available for 3DEG)

Asymmetric/Biological Unit(hide GO term definitions)

Chain C (LEPA_ECOLI | P60785)

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:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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:0043023	ribosomal large subunit binding	Interacting selectively and non-covalently with any part of the larger ribosomal subunit.
	GO:0043024	ribosomal small subunit binding	Interacting selectively and non-covalently with any part of the small ribosomal subunit.
	GO:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0045727	positive regulation of translation	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0009409	response to cold	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
	GO:0009268	response to pH	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus. pH is a measure of the acidity or basicity of an aqueous solution.
	GO:0009651	response to salt stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain D (RS12_ECOLI | P0A7S3)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0034336	misfolded RNA binding	Interacting selectively and non-covalently with an RNA molecule that has assumed an incorrect conformation.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0000372	Group I intron splicing	The splicing of Group I introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group I introns and involved in determining the locations of the splice sites (there do not appear to be consensus splice site sequences) as well as having a role in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions, generally with exogenous guanosine as the initiating nucleophile. The intron is excised as a linear piece (though it may subsequently circularize).
	GO:0034337	RNA folding	The process of assisting in the covalent and noncovalent assembly of single or multimeric RNAs into the correct tertiary structure.
	GO:0033120	positive regulation of RNA splicing	Any process that activates or increases the frequency, rate or extent of RNA splicing.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	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:0022627	cytosolic small ribosomal subunit	The small 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.
	GO:0015935	small ribosomal subunit	The smaller of the two subunits of a ribosome.

Chain H (RL11_ECOLI | P0A7J7)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0015968	stringent response	A specific global change in the metabolism of a bacterial cell (the downregulation of nucleic acid and protein synthesis, and the simultaneous upregulation of protein degradation and amino acid synthesis) as a result of starvation.
	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:0006415	translational termination	The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
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: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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		1MA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		2MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		YG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 3deg)

	Cis Peptide Bonds
		Gly C:30 - Leu C:31	[ RasMol ]
		Thr C:241 - Pro C:242	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3DEG)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (11, 15)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (37, 47)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File