1Y39 | PR0144 - JenaLib

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Description

Title :   CO-EVOLUTION OF PROTEIN AND RNA STRUCTURES WITHIN A HIGHLY CONSERVED RIBOSOMAL DOMAIN

Authors :   M. S. Dunstan, D. Guhathakurta, D. E. Draper, G. L. Conn

Date :   24 Nov 04 (Deposition) - 22 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   X-Ray Crystal Structure, Choroplast-Like L11 Complex, Rrna, 23S Rna, Structural Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. S. Dunstan, D. Guhathakurta, D. E. Draper, G. L. Conn
Coevolution Of Protein And Rna Structures Within A Highly Conserved Ribosomal Domain
Chem. Biol. V. 12 201 2005
PubMed-ID: 15734647 | Reference-DOI: 10.1016/J.CHEMBIOL.2004.11.019

Compounds

Molecule 1 - 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
	Chains	:	C, D
	Engineered	:	YES
	Mutation	:	YES
	Other Details	:	NTS 1051-1108 FROM E. COLI 23S RRNA
	Synthetic	:	YES

Molecule 2 - 50S RIBOSOMAL PROTEIN L11
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	L11-C76(S69N)
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PUC18
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11
	Mutation	:	YES
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422
	Synonym	:	RIBOSOMAL PROTEIN L11

Structural Features

Chains, Units

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (5, 26)

Asymmetric Unit (5, 26)

No.	Name	Count	Type	Full Name
1	3CO	2	Ligand/Ion	COBALT (III) ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	GTP	2	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
4	K	2	Ligand/Ion	POTASSIUM ION
5	MG	18	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	3CO	1	Ligand/Ion	COBALT (III) ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
4	K	-1	Ligand/Ion	POTASSIUM ION
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	3CO	1	Ligand/Ion	COBALT (III) ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
4	K	-1	Ligand/Ion	POTASSIUM ION
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (20, 20)

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	G D:337	BINDING SITE FOR RESIDUE 3CO D 401
02	AC2	SOFTWARE	A D:319 , A D:320 , C D:322 , A D:323 , GOL D:704	BINDING SITE FOR RESIDUE K D 403
03	AC3	SOFTWARE	A C:119 , A C:120 , C C:122 , A C:123 , MG C:415	BINDING SITE FOR RESIDUE K C 404
04	AC4	SOFTWARE	A C:123 , G C:143 , U C:144	BINDING SITE FOR RESIDUE MG C 405
05	AC5	SOFTWARE	G D:313 , A D:320 , C D:322	BINDING SITE FOR RESIDUE MG D 406
06	AC6	SOFTWARE	U C:115 , U C:116 , A D:336	BINDING SITE FOR RESIDUE MG C 407
07	AC7	SOFTWARE	G C:113	BINDING SITE FOR RESIDUE MG C 408
08	AC8	SOFTWARE	A C:104 , G C:106 , HOH C:806	BINDING SITE FOR RESIDUE MG C 409
09	AC9	SOFTWARE	HOH D:811	BINDING SITE FOR RESIDUE MG D 410
10	BC1	SOFTWARE	A D:307 , A D:336 , G D:337 , HOH D:810	BINDING SITE FOR RESIDUE MG D 411
11	BC2	SOFTWARE	U D:308 , U D:310 , HOH D:809	BINDING SITE FOR RESIDUE MG D 412
12	BC3	SOFTWARE	G D:306	BINDING SITE FOR RESIDUE MG D 413
13	BC4	SOFTWARE	A C:120 , C C:122 , K C:404	BINDING SITE FOR RESIDUE MG C 415
14	BC5	SOFTWARE	G C:121	BINDING SITE FOR RESIDUE MG C 416
15	BC6	SOFTWARE	U D:308 , A D:311	BINDING SITE FOR RESIDUE MG D 418
16	BC7	SOFTWARE	U C:110	BINDING SITE FOR RESIDUE MG C 420
17	BC8	SOFTWARE	G C:106 , A C:107 , A C:136 , G C:137 , HOH C:807	BINDING SITE FOR RESIDUE MG C 421
18	BC9	SOFTWARE	G D:313 , A D:320	BINDING SITE FOR RESIDUE MG D 422
19	CC1	SOFTWARE	A D:319 , C D:322 , A D:323 , G D:343 , U D:344 , A D:346 , U D:347 , K D:403	BINDING SITE FOR RESIDUE GOL D 704
20	CC2	SOFTWARE	GTP C:101 , G C:157 , GTP D:301 , U D:358	BINDING SITE FOR RESIDUE GOL C 705

SS Bonds (0, 0)

(no "SS Bond" information available for 1Y39)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1Y39)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y39)

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L11	PS00359	Ribosomal protein L11 signature.	RL11_GEOSE	118-133	2	A:61-75 B:261-276

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L11	PS00359	Ribosomal protein L11 signature.	RL11_GEOSE	118-133	1	A:61-75 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L11	PS00359	Ribosomal protein L11 signature.	RL11_GEOSE	118-133	1	- B:261-276

Exons (0, 0)

(no "Exon" information available for 1Y39)

Sequences/Alignments

Asymmetric 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:74
 aligned with RL11_GEOSE | P56210 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:74
                                    68        78        88        98       108       118       128    
           RL11_GEOSE    59 TFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGIVVE 132
               SCOP domains d1y39a1 A:2-75 Ribosomal protein L11, C-terminal domain                    SCOP domains
               CATH domains 1y39A00 A:2-75  [code=1.10.10.250, no name defined]                        CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.............eeehhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------RIBOSOMAL_L11   PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 1y39 A   2 TFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARNMGIVVE  75
                                    11        21        31        41        51        61        71

Chain B from PDB  Type:PROTEIN  Length:72
 aligned with RL11_GEOSE | P56210 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:72
                                    71        81        91       101       111       121       131  
           RL11_GEOSE    62 TKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGIVVED 133
               SCOP domains d1y39b1 B:205-275 Ribosomal protein L11, C-terminal domain             - SCOP domains
               CATH domains 1y39B00 B:205-276  [code=1.10.10.250, no name defined]                   CATH domains
           Pfam domains (1) -Ribosomal_L11-1y39B01 B:206-274                                      -- Pfam domains (1)
           Pfam domains (2) -Ribosomal_L11-1y39B02 B:206-274                                      -- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhh..............eeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------RIBOSOMAL_L11    PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 1y39 B 205 TKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARNMGIVVED 276
                                   214       224       234       244       254       264       274

Chain C from PDB  Type:RNA  Length:58
                                                                                          
                 1y39 C 101 gCCAGGAUGUAUGCUUAGAAGCAGCAAUCAUUUAAAGAGUGCGUAAUAGCUCACUGGU 158
                            |      110       120       130       140       150        
                          101-GTP

Chain D from PDB  Type:RNA  Length:58
                                                                                          
                 1y39 D 301 gCCAGGAUGUAUGCUUAGAAGCAGCAAUCAUUUAAAGAGUGCGUAAUAGCUCACUGGU 358
                            |      310       320       330       340       350        
                          301-GTP

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, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Ribosomal protein L11, C-terminal domain (96)

Family: Ribosomal protein L11, C-terminal domain (96)

Protein domain: Ribosomal protein L11, C-terminal domain (96)

Bacillus stearothermophilus [TaxId: 1422] (8)

1a	d1y39a1	A:2-75
1b	d1y39b1	B:205-275

CATH Domains (1, 2)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: [code=1.10.10.250, no name defined] (69)

[unclassified] (3)

1a	1y39B00	B:205-276
1b	1y39A00	A:2-75

Pfam Domains (1, 2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Ribosomal_L11] (35)

Family: Ribosomal_L11 (35)

Geobacillus stearothermophilus (Bacillus stearothermophilus) (2)

1a	Ribosomal_L11-1y39B01	B:206-274
1b	Ribosomal_L11-1y39B02	B:206-274

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RL11_GEOSE | P56210)

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: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.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	RL11_GEOSE \| P56210	:	1aci 1c04 1fow 1fox 1foy 1hc8 1ip8 1qa6 2fow

Related Entries Specified in the PDB File

1hc8	CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX