1PN8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   COORDINATES OF S12, L11 PROTEINS AND E-SITE TRNA FROM 70S CRYSTAL STRUCTURE SEPARATELY FITTED INTO THE CRYO-EM MAP OF E.COLI 70S.EF-G.GDPNP COMPLEX. THE ATOMIC COORDINATES ORIGINALLY FROM THE E-SITE TRNA WERE FITTED IN THE POSITION OF THE HYBRID P/E-SITE TRNA.

Authors :   M. Valle, A. Zavialov, J. Sengupta, U. Rawat, M. Ehrenberg, J. Frank

Date :   12 Jun 03 (Deposition) - 15 Jul 03 (Release) - 02 Feb 10 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   10.80

Chains :   Asym./Biol. Unit : D,L,O

Keywords :   Ribosomal Protein, Trna Binding Protein, Trna, Rna Binding Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Valle, A. Zavialov, J. Sengupta, U. Rawat, M. Ehrenberg, J. Frank
Locking And Unlocking Of Ribosomal Motions
Cell(Cambridge, Mass. ) V. 114 123 2003
PubMed-ID: 12859903 | Reference-DOI: 10.1016/S0092-8674(03)00476-8

Molecule 1 - E-TRNA
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - 30S RIBOSOMAL PROTEIN S12
	Chains	:	O
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

Molecule 3 - 50S RIBOSOMAL PROTEIN L11
	Chains	:	L
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

		1	2	3
Asymmetric/Biological Unit	:	D	L	O

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1PN8)

(no "Site" information available for 1PN8)

(no "SS Bond" information available for 1PN8)

(no "Cis Peptide Bond" information available for 1PN8)

(no "SAP(SNP)/Variant" information available for 1PN8)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S12	PS00055	Ribosomal protein S12 signature.	RS12_THET8	43-50	1	O:46-53
2	RIBOSOMAL_L11	PS00359	Ribosomal protein L11 signature.	RL11_THEMA	126-141	1	L:126-140

(no "Exon" information available for 1PN8)

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 D from PDB  Type:RNA  Length:68
                                                                                                    
                 1pn8 D   1 UCCGUGAAACAAAGCGGAUGUACCGGAUUUUUAUUCCGGCUAUGGGGCAAUUCCCCGUCGCGGAGCCA  76
                                  ||11    ||||24        34        44 |||  ||58        68        
                                  7|     16|||                      46|| 53|                    
                                   9      18||                       48|  56                    
                                           19|                        50                        
                                            22

Chain L 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 d1pn8l_ L: 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
                 1pn8 L   8 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV 140
                                    17        27        37        47        57        67        77        87        97       107       117       127       137

Chain O from PDB  Type:PROTEIN  Length:124
 aligned with RS12_THET8 | Q5SHN3 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
           RS12_THET8     2 PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEA 125
               SCOP domains d1pn8o_ O: 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 -----------------------------------------RIBOSOMA--------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pn8 O   5 PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEA 128
                                    14        24        34        44        54        64        74        84        94       104       114       124

Legend:		→ Mismatch	(orange background)
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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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Low resolution protein structures (283)

Fold: Ribosome and ribosomal fragments (154)

Superfamily: Ribosome and ribosomal fragments (154)

Family: Ribosome complexes (103)

Protein domain: 70S ribosome functional complex (103)

Escherichia coli [TaxId: 562] (72)

1a	d1pn8l_	L:
1b	d1pn8o_	O:

(no "CATH Domain" information available for 1PN8)

(no "Pfam Domain" information available for 1PN8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain L (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 O (RS12_THET8 | Q5SHN3)

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.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
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.
	GO:0015935	small ribosomal subunit	The smaller of the two subunits of a ribosome.

Asymmetric/Biological Unit
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1gix	CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5A RESOLUTION -- 30S RIBOSOME SUBUNIT, THREE TRNA, AND MRNA MOLECULES
1giy	CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5A RESOLUTION -- 50S RIBOSOME SUBUNIT
1pn6	ELONGATION FACTOR-G, E.COLI 70S RIBOSOME, POST-TERMINATION COMPLEX, FITTING OF CRYSTAL STRUCTURE, CRYO-EM
1pn7	COORDINATES OF S12, L11 PROTEINS AND P-TRNA, FROM THE 70S X -RAY STRUCTURE ALIGNED TO THE 70S CRYO-EM MAP OF E.COLI RIBOSOME RELATED ID: EMD-1055 RELATED DB: EMDB RELATED ID: EMD-1362 RELATED DB: EMDB RELATED ID: EMD-1363 RELATED DB: EMDB RELATED ID: EMD-1364 RELATED DB: EMDB RELATED ID: EMD-1365 RELATED DB: EMDB RELATED ID: EMD-1366 RELATED DB: EMDB

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