2VRH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF THE E. COLI TRIGGER FACTOR BOUND TO A TRANSLATING RIBOSOME

Authors :   F. Merz, D. Boehringer, C. Schaffitzel, S. Preissler, A. Hoffmann, T. Maier, A. Rutkowska, J. Lozza, N. Ban, B. Bukau, E. Deuerling

Date :   07 Apr 08 (Deposition) - 17 Jun 08 (Release) - 07 Aug 13 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   19.00

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

Keywords :   Ribosome, Trigger Factor, Ribosomal Protein, Ribonucleoprotein, Co-Translational Protein Folding, Rotamase, Chaperone, Isomerase, Cell Cycle, Rna-Binding, Rrna-Binding, Cell Division, Ribosome-Nascent Chain Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Merz, D. Boehringer, C. Schaffitzel, S. Preissler, A. Hoffmann, T. Maier, A. Rutkowska, J. Lozza, N. Ban, B. Bukau, E. Deuerling
Molecular Mechanism And Structure Of Trigger Factor Bound To The Translating Ribosome.
Embo J. V. 27 1622 2008
PubMed-ID: 18497744 | Reference-DOI: 10.1038/EMBOJ.2008.89

Molecule 1 - TRIGGER FACTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	BASED ON PDB 1W26_A. RESIDUES 22-62 WERE REPLACED WITH THE CORRESPONDING RESIDUES OF PDB 1OMS_B
	Other Details - Source	:	BASED ON PDB 1W26_A

Molecule 2 - 50S RIBOSOMAL PROTEIN L23
	Chains	:	B
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	BASED ON PDB 2AW4_T
	Other Details - Source	:	BASED ON PDB 2AW4_T

Molecule 3 - 50S RIBOSOMAL PROTEIN L24
	Chains	:	C
	Fragment	:	RESIDUES 2-104
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	BASED ON PDB 2AW4_U
	Other Details - Source	:	BASED ON PDB 2AW4_U

Molecule 4 - 50S RIBOSOMAL PROTEIN L29
	Chains	:	D
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	BASED ON PDB 2AW4_X
	Other Details - Source	:	BASED ON PDB 2AW4_X

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 11)

No.	Name	Count	Type	Full Name
1	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2VRH)

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

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

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

Asymmetric/Biological Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L24	PS01108	Ribosomal protein L24 signature.	RL24_ECOLI	8-25	1	C:7-24
2	RIBOSOMAL_L29	PS00579	Ribosomal protein L29 signature.	RL29_ECOLI	39-53	1	D:39-53
3	RIBOSOMAL_L23	PS00050	Ribosomal protein L23 signature.	RL23_ECOL5	81-96	1	B:81-96
3	RIBOSOMAL_L23	PS00050	Ribosomal protein L23 signature.	RL23_ECOLI	81-96	1	B:81-96
4	FKBP_PPIASE	PS50059	FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.	TIG_ECOLI	161-249	1	A:161-249

(no "Exon" information available for 2VRH)

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:431
 aligned with TIG_ECOLI | P0A850 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:431
                                    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 
            TIG_ECOLI     1 MQVSVETTQGLGRRVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPMNIVAQRYGASVRQDVLGDLMSRNFIDAIIKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEVELQGLEAIEVEKPIVEVTDADVDGMLDTLRKQQATWKEKDGAVEAEDRVTIDFTGSVDGEEFEGGKASDFVLAMGQGRMIPGFEDGIKGHKAGEEFTIDVTFPEEYHAENLKGKAAKFAINLKKVEERELPELTAEFIKRFGVEDGSVEGLRAEVRKNMERELKSAIRNRVKSQAIEGLVKANDIDVPAALIDSEIDVLRRQAAQRFGGNEKQALELPRELFEEQAKRRVVVGLLLGEVIRTNELKADEERVKGLIEEMASAYEDPKEVIEFYSKNKELMDNMRNVALEEQAVEAVLAKAKVTEKETTFNELMNQQ 431
               SCOP domains d2vrha2 A:1-131 Trigger factor ribosome-binding domain                                                                             d2vrha3 A:132-247 Trigger factor PPIase domain                                                                      d2vrha1 A:248-431 Trigger factor, C-terminal domain                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................................................................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------FKBP_PPIASE  PDB: A:161-249 UniProt: 161-249                                             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vrh A   1 mQVSVETTQGLGRRVTITIAADSIETAVKSELVNVAKKVRIDGFRKGKVPmNIVAQRYGASVRQDVLGDLmSRNFIDAIIKEKINPAGAPTYVPGEYKLGEDFTYSVEFEVYPEVELQGLEAIEVEKPIVEVTDADVDGmLDTLRKQQATWKEKDGAVEAEDRVTIDFTGSVDGEEFEGGKASDFVLAmGQGRmIPGFEDGIKGHKAGEEFTIDVTFPEEYHAENLKGKAAKFAINLKKVEERELPELTAEFIKRFGVEDGSVEGLRAEVRKNmERELKSAIRNRVKSQAIEGLVKANDIDVPAALIDSEIDVLRRQAAQRFGGNEKQALELPRELFEEQAKRRVVVGLLLGEVIRTNELKADEERVKGLIEEmASAYEDPKEVIEFYSKNKELmDNmRNVALEEQAVEAVLAKAKVTEKETTFNELmNQQ 431
                            |       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 
                            1-MSE                                            51-MSE              71-MSE                                                              140-MSE                                          189-MSE|                                                                             274-MSE                                                                                             374-MSE              395-MSE                          428-MSE
                                                                                                                                                                                                                           194-MSE                                                                                                                                                                                                     398-MSE

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with RL23_ECOL5 | Q0TCE3 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
           RL23_ECOL5     1 MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNLDFVGGA  99
               SCOP domains d2vrhb1 B:1-99 Ribosomal protein L23                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------RIBOSOMAL_L23   --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 2vrh B   1 MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNLDFVGGA  99
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with RL23_ECOLI | P0ADZ0 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
           RL23_ECOLI     1 MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNLDFVGGA  99
               SCOP domains d2vrhb1 B:1-99 Ribosomal protein L23                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------RIBOSOMAL_L23   --- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 2vrh B   1 MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNLDFVGGA  99
                                    10        20        30        40        50        60        70        80        90

Chain C from PDB  Type:PROTEIN  Length:102
 aligned with RL24_ECOLI | P60624 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:102
                                    11        21        31        41        51        61        71        81        91       101  
           RL24_ECOLI     2 AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETI 103
               SCOP domains d2vrhc1 C:1-102 Ribosomal proteins L24 (L24p)                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------RIBOSOMAL_L24     ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2vrh C   1 AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETI 102
                                    10        20        30        40        50        60        70        80        90       100

Chain D from PDB  Type:PROTEIN  Length:63
 aligned with RL29_ECOLI | P0A7M6 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:63
                                    10        20        30        40        50        60   
           RL29_ECOLI     1 MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA  63
               SCOP domains d2vrhd1 D:1-63 Ribosomal protein L29 (L29p)                     SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------RIBOSOMAL_L29  ---------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 2vrh D   1 MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA  63
                                    10        20        30        40        50        60

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 2VRH)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TIG_ECOLI | P0A850)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0003755	peptidyl-prolyl cis-trans isomerase activity	Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
	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:0044183	protein binding involved in protein folding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) that contributes to the process of protein folding.
	GO:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
biological process
	GO:0051083	'de novo' cotranslational protein folding	The process of assisting in the correct noncovalent assembly of the ribosome-bound nascent chains of a multidomain protein whilst other parts of the protein are still being translated.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0061077	chaperone-mediated protein folding	The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0000413	protein peptidyl-prolyl isomerization	The modification of a protein by cis-trans isomerization of a proline residue.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0043335	protein unfolding	The process of assisting in the disassembly of non-covalent linkages in a protein or protein aggregate, often where the proteins are in a non-functional or denatured state.
	GO:0009408	response to heat	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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Chain B (RL23_ECOLI | P0ADZ0)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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: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: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 B (RL23_ECOL5 | Q0TCE3)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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: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: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 (RL24_ECOLI | P60624)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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 D (RL29_ECOLI | P0A7M6)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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: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.

Asymmetric/Biological Unit
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Access by PDB/NDB ID
	2vrh
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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Access by UniProt ID/Accession number
	RL23_ECOL5 \| Q0TCE3
		Comparative Protein Structure Models	:	ModBase
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		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RL23_ECOLI \| P0ADZ0
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		Protein-protein Interaction	:	DIP
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	RL24_ECOLI \| P60624
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		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RL29_ECOLI \| P0A7M6
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		Protein-protein Interaction	:	DIP
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	TIG_ECOLI \| P0A850
		Comparative Protein Structure Models	:	ModBase
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1l1p	SOLUTION STRUCTURE OF THE PPIASE DOMAIN FROM E. COLITRIGGER FACTOR RELATED ID: EMD-1499 RELATED DB: EMDB STRUCTURE OF THE E. COLI TRIGGER FACTOR BOUND TO A TRANSLATING RIBOSOME
1oms	STRUCTURE DETERMINATION BY MAD: E.COLI TRIGGER FACTORBINDING AT THE RIBOSOMAL EXIT TUNNEL.
1p85	REAL SPACE REFINED COORDINATES OF THE 50S SUBUNIT FITTEDINTO THE LOW RESOLUTION CRYO-EM MAP OF THE EF -G.GTP STATEOF E. COLI 70S RIBOSOME
1p86	REAL SPACE REFINED COORDINATES OF THE 50S SUBUNIT FITTEDINTO THE LOW RESOLUTION CRYO-EM MAP OF THE INITIATION-LIKESTATE OF E. COLI 70S RIBOSOME
1p9y	RIBOSOME BINDING OF E. COLI TRIGGER FACTOR MUTANT F44L.
1w26	TRIGGER FACTOR IN COMPLEX WITH THE RIBOSOME FORMS A MOLECULAR CRADLE FOR NASCENT PROTEINS
1w2b	TRIGGER FACTOR RIBOSOME BINDING DOMAIN IN COMPLEX WITH 50S
2aw4	CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROMESCHERICHIA COLI AT 3.5 A RESOLUTION. THIS FILE CONTAINSTHE 50S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTALSTRUCTURE CONTAINS TWO 70S RIBOSOMES AND IS DESCRIBED INREMARK 400.
2awb	CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROMESCHERICHIA COLI AT 3.5 A RESOLUTION. THIS FILE CONTAINSTHE 50S SUBUNIT OF THE SECOND 70S RIBOSOME. THE ENTIRECRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES AND ISDESCRIBED IN REMARK 400.
2j28	MODEL OF E. COLI SRP BOUND TO 70S RNCS
2vhm	STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME
2vhn	STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME
2wwq	E.COLI 70S RIBOSOME STALLED DURING TRANSLATION OF TNAC LEADER PEPTIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 11)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (4, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (6, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (28, 54)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File