1MZP | PR0085 - JenaLib

Title :   STRUCTURE OF THE L1 PROTUBERANCE IN THE RIBOSOME

Authors :   A. Nikulin, I. Eliseikina, S. Tishchenko, N. Nevskaya, N. Davydova, O. Platonova, W. Piendl, M. Selmer, A. Liljas, R. Zimmermann, M. Garber, S. Nikonov

Date :   09 Oct 02 (Deposition) - 21 Jan 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

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

Keywords :   Ribosome, Ribosomal Protein, Rna-Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Nikulin, I. Eliseikina, S. Tishchenko, N. Nevskaya, N. Davydova, O. Platonova, W. Piendl, M. Selmer, A. Liljas, D. Drygin, R. Zimmermann, M. Garber, S. Nikonov
Structure Of The L1 Protuberance In The Ribosome.
Nat. Struct. Biol. V. 10 104 2003
PubMed-ID: 12514741 | Reference-DOI: 10.1038/NSB886
(for further references see the PDB file header)

Compounds

Molecule 1 - FRAGMENT OF 23S RRNA
	Chains	:	B
	Engineered	:	YES
	Other Details	:	SYNTHESIS OF THE RNA FRAGMENT FROM THE PLASMID PDD55; SEQUENCE FROM CELL-FREE(IN VITRO) SYSTEM WITHOUT LIVING ORGANISM.
	Synthetic	:	YES

Molecule 2 - 50S RIBOSOMAL PROTEIN L1P
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSACL1.4
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SULFOLOBUS ACIDOCALDARIUS
	Organism Taxid	:	2285
	Other Details	:	AUTHOR STATES TO AVOID THE POTENTIAL MISINCORPORATION OF LYSINE INSTEAD OF ARGININE, THE HOST STRAIN WAS COTRANSFORMED WITH PUBS520, A PLASMID CARRYING THE GENE FOR TRNA(ARG)AGA-AGG.

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:217
 aligned with RL1_SULAC | P35024 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:217
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       
            RL1_SULAC     4 VLADKESLIEALKLALSTEYNVKRNFTQSVEIILTFKGIDMKKGDLKLREIVPLPKQPSKAKRVLVVPSFEQLEYAKKASPNVVITREELQKLQGQKRPVKKLARQNEWFLINQESMALAGRILGPALGPRGKFPTPLPNTADISEYINRFKRSVLVKTKDQPQVQVFIGTEDMKPEDLAENAIAVLNAIENKAKVETNLRNIYVKTTMGKAVKVKR 220
               SCOP domains d1mzpa_ A: Ribosomal protein L1                                                                                                                                                                                           SCOP domains
               CATH domains 1mzpA01 A:1-61,A:153-217  [code=3.30.190.20, no name defined]1mzpA02 A:62-152  [code=3.40.50.790, no name defined]                                      1mzpA01 A:1-61,A:153-217  [code=3.30.190.20, no name defined]     CATH domains
               Pfam domains --Ribosomal_L1-1mzpA01 A:3-212                                                                                                                                                                                      ----- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh...........eeeeeeee...hhhhh....eeeee..........eeee.hhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhheeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhh.....eeeeeeee.....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L1        --------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mzp A   1 MLADKESLIEALKLALSTEYNVKRNFTQSVEIILTFKGIDmKKGDLKLREIVPLPKQPSKAKRVLVVPSSEQLEYAKKASPKVVITREELQKLQGQKRPVKKLARQNEWFLINQESmALAGRILGPALGPRGKFPTPLPNTADISEYINRFKRSVLVKTKDQPQVQVFIGTEDmKPEDLAENAIAVLNAIENKAKVETNLRNIYVKTTmGKAVKVKR 217
                                    10        20        30        40|       50        60        70        80        90       100       110      |120       130       140       150       160       170   |   180       190       200       210       
                                                                   41-MSE                                                                     117-MSE                                                  174-MSE                            209-MSE

Chain B from PDB  Type:RNA  Length:55
                                                                                       
                 1mzp B   1 GGGAUGCGUAGGAUAGGUGGGAGCCGCAAGGCGCCGGUGAAAUACCACCCUUCCC  55
                                    10        20        30        40        50

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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RL1_SULAC | P35024)

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:0006417	regulation of translation	Any process that modulates 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: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:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0015934	large ribosomal subunit	The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
	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.

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