2JQ7 - JenaLib

Title :   MODEL FOR THIOSTREPTON BINDING TO THE RIBOSOMAL L11-RNA

Authors :   H. R. A. Jonker, S. Ilin, S. K. Grimm, J. Woehnert, H. Schwalbe

Date :   30 May 07 (Deposition) - 03 Jul 07 (Release) - 27 May 15 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C  (10x)
NMR Structure *: A,B,C  (1x)

Keywords :   Ribosome-Antibiotic Complex, Thiopeptide, Antibacterial, Thiazole, Thiazoline, Oxazole, Ribosome, L11, Translation Inhibition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. R. A. Jonker, S. Ilin, S. K. Grimm, J. Woehnert, H. Schwalbe
L11 Domain Rearrangement Upon Binding To Rna And Thiostrepton Studied By Nmr Spectroscopy
Nucleic Acids Res. V. 35 441 2007
PubMed-ID: 17169991 | Reference-DOI: 10.1093/NAR/GKL1066

Compounds

Molecule 1 - 50S RIBOSOMAL PROTEIN L11
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	RPLK
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

Molecule 2 - RIBOSOMAL RNA
	Chains	:	B
	Engineered	:	YES
	Fragment	:	L11 BINDING DOMAIN, RESIDUES 1051-1108
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	IN VITRO TRANSCRIBED RNA CONSTRUCT.
	Synthetic	:	YES

Molecule 3 - THIOSTREPTON
	Chains	:	C
	Organism Scientific	:	STREPTOMYCES AZUREUS
	Organism Taxid	:	146537

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 13)

NMR Structure (8, 13)

No.	Name	Count	Type	Full Name
1	BB9	4	Mod. Amino Acid	(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
2	DBU	1	Mod. Amino Acid	(2Z)-2-AMINOBUT-2-ENOIC ACID
3	DCY	1	Mod. Amino Acid	D-CYSTEINE
4	DHA	3	Mod. Amino Acid	2-AMINO-ACRYLIC ACID
5	MH6	1	Mod. Amino Acid	3-HYDROXY-2-IMINOPROPANOIC ACID
6	NH2	1	Mod. Amino Acid	AMINO GROUP
7	QUA	1	Mod. Amino Acid	8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID
8	TS9	1	Mod. Amino Acid	(2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC ACID

NMR Structure * (8, 13)

No.	Name	Count	Type	Full Name
1	BB9	4	Mod. Amino Acid	(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
2	DBU	1	Mod. Amino Acid	(2Z)-2-AMINOBUT-2-ENOIC ACID
3	DCY	1	Mod. Amino Acid	D-CYSTEINE
4	DHA	3	Mod. Amino Acid	2-AMINO-ACRYLIC ACID
5	MH6	1	Mod. Amino Acid	3-HYDROXY-2-IMINOPROPANOIC ACID
6	NH2	1	Mod. Amino Acid	AMINO GROUP
7	QUA	1	Mod. Amino Acid	8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID
8	TS9	1	Mod. Amino Acid	(2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC ACID

Sites (1, 1)

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

NMR Structure

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:134
 aligned with RL11_THEMA | P29395 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:134
                                    17        27        37        47        57        67        77        87        97       107       117       127       137    
          RL11_THEMA      8 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVVD  141
               SCOP domains d2jq7a1 A:8-140 70S ribosome functional complex                                                                                      - SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee...hhhhhhhhhhh.............eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L11    PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2jq7 A    8 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVVD  141
                                    17        27        37        47        57        67        77        87        97       107       117       127       137

Chain B from PDB  Type:RNA  Length:58
                                                                                           
                2jq7 B 1051 GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC 1108
                                  1060      1070      1080      1090      1100

Chain C from PDB  Type:PROTEIN  Length:19
 aligned with THCL_STRAJ | P0C8P8 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:19
                                            72  
                                    64       | 
          THCL_STRAJ     55 MIASASCTTCICTCSCSS-    -
               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
                2jq7 C    0 xIAsAScTtxicTcscssx   18
                            |  |  | |9|| ||||||
                            0-QUA | |||| |15-BB9
                               3-DHA|||| ||16-DHA
                                  6-BB9| || 17-DHA
                                    8-DBU||  18-NH2
                                     9-DCY|    
                                     10-TS9    
                                      11-BB9   
                                        13-BB9 
                                         14-MH6

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

NMR Structure(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 C (THCL_STRAJ | P0C8P8)

biological process
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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Description