1OLN - JenaLib

Title :   MODEL FOR THIOSTREPTON ANTIBIOTIC BINDING TO L11 SUBSTRATE FROM 50S RIBOSOMAL RNA

Authors :   G. Lentzen, R. Klinck, N. Matassova, F. Aboul-Ela, A. I. H. Murchie

Date :   08 Aug 03 (Deposition) - 11 Sep 03 (Release) - 13 Jul 11 (Revision)

Method :   SOLUTION NMR; THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A,B,C
Biol. Unit 1: A,B,C  (1x)

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

Reference :   G. Lentzen, R. Klinck, N. Matassova, F. Aboul-Ela, A. I. H. Murchie
Structural Basis For Contrasting Activities Of Ribosome Binding Thiazole Antibiotics
Chem. Biol. V. 10 769 2003
PubMed-ID: 12954336 | Reference-DOI: 10.1016/S1074-5521(03)00173-X
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 13)

Theoretical Model (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	(2E)-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

Theoretical Model 1 (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	(2E)-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

Theoretical Model

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: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 d1olna_ A: Ribosomal L11 protein in complex with thiostrepton and a 23S rRNA fragment                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Ribosomal_L11_N-1olnA02 A:8-66                             ----Ribosomal_L11-1olnA01 A:71-139                                       - Pfam domains
         Sec.struct. author .eeeeee..........hhhhhh...hhhhhhhhhhhhh......eeeeeeee.....eeeee...hhhhhhhhhhh.............eeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L11   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1oln A    8 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV  140
                                    17        27        37        47        57        67        77        87        97       107       117       127       137

Chain B 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
                1oln B    0 xIAsAScTtcicTcscssx   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

Chain C from PDB  Type:RNA  Length:58
                                                                                           
                1oln C 1051 GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC 1108
                                  1060      1070      1080      1090      1100

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 (2, 2)

Gene Ontology (11, 11)

Theoretical Model(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 B (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.

Visualization

Interactive Views

Theoretical Model
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BB9	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DBU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DCY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DHA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MH6	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NH2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		QUA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TS9	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1oln)

Biological Unit
	Complete Structure
		Theoretical Model 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1oln
		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)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RL11_THEMA \| P29395
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	THCL_STRAJ \| P0C8P8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RL11_THEMA \| P29395
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	THCL_STRAJ \| P0C8P8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1jqs	FITTING OF L11 PROTEIN AND ELONGATION FACTOR G (DOMAIN G'AND V) IN THE CRYO-EM MAP OF E. COLI 70S RIBOSOME BOUNDWITH EF-G AND GMPPCP
1d8t	CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-MGGDP COMPLEXED WITH THE THIOPEPTIDE GE2270A.
1e9w	CRYSTAL STRUCTURE OF THIOPEPTIDE THIOSTREPTON
1eg0	FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E. COLI 70S RIBOSOME
1giy	CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5A RESOLUTIO
1jqm	FITTING OF L11 PROTEIN AND ELONGATION FACTOR G (EF-G) IN THE CRYO-EM MAP OF E. COLI 70S RIBOSOME BOUND WITH EF-G,GDP AND FUSIDIC ACID
1jqt	FITTING OF L11 PROTEIN IN THE LOW RESOLUTION CRYO-EM MAP OFE.COLI 70S RIBOSOME
1mms	CRYSTAL STRUCTURE OF THE RIBOSOMAL PROTEIN L11-RNA COMPLEX
1pn7	COORDINATES OF S12, L11 PROTEINS AND P-TRNA, FROM THE 70S X-RAY STRUCTURE ALIGNED TO THE 70S CRYO-EM MAP OF E. COLIRIBOSOME
1pn8	COORDINATES OF S12, L11 PROTEINS AND E-SITE TRNA FROM 70S CRYSTAL STRUCTURE SEPARATELY FITTED INTO THE CRYO-EM MAPOF E.COLI 70S.EF-G.GDPNP COMPLEX. THE COORDINATESORIGINALLY FROM THE E-SITE TRNA WERE FITTED IN THEPOSITION OF THE HYBRID P /E-SITE TRNA.
2c77	CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-GNP COMPLEXED WITH THIOPEPTIDE GE2270A.
2jq7	SOLUTION STRUCTURE OF THE COMPLEX OF THIOPEPTIDE THIOSTREPTON AND RIBOSOMAL L11-RNA
2zjp	CRYSTAL STRUCTURE OF NOSIHEPTIDE COMPLEXED WITH THE LARGE RIBOSOMAL SUBUNIT OF DEINOCOCCUS RADIODURANS
3cf5	CRYSTAL STRUCTURE OF RIBOSOMAL L11-RNA COMPLEXED WITH THE THIOPEPTIDE THIOSTREPTON
487d	SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-EM MAP OF THE LARGE 50S SUBUNIT AT 7.5 A.

Description