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Description

Title :   CRYSTAL STRUCTURE OF THE RIBOSOMAL PROTEIN L11-RNA COMPLEX

Authors :   B. T. Wimberly, R. Guymon, J. P. Mccutcheon, S. W. White, V. Ramakrishna

Date :   14 Apr 99 (Deposition) - 17 Apr 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.57

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

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

Reference :   B. T. Wimberly, R. Guymon, J. P. Mccutcheon, S. W. White, V. Ramakrishnan
A Detailed View Of A Ribosomal Active Site: The Structure O The L11-Rna Complex.
Cell(Cambridge, Mass. ) V. 97 491 1999
PubMed-ID: 10338213 | Reference-DOI: 10.1016/S0092-8674(00)80759-X
(for further references see the PDB file header)

Compounds

Molecule 1 - 23S RIBOSOMAL RNA
	Chains	:	C, D
	Engineered	:	YES
	Fragment	:	RESIDUES 1051-1108
	Mutation	:	YES
	Other Details	:	COVALENT MERCURY LIGAND AT U1061
	Other Details - Source	:	IN VITRO TRANSCRIBED RRNA FROM THERMOTOGA MARITIMA
	Synthetic	:	YES

Molecule 2 - PROTEIN (RIBOSOMAL PROTEIN L11)
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET13A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Other Details	:	COVALENT MERCURY LIGAND AT CYS39
	Other Details - Source	:	RECOMBINANT PROTEIN

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 (3, 35)

Asymmetric Unit (3, 35)

No.	Name	Count	Type	Full Name
1	CD	8	Ligand/Ion	CADMIUM ION
2	MG	19	Ligand/Ion	MAGNESIUM ION
3	MMC	8	Ligand/Ion	METHYL MERCURY ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MMC	5	Ligand/Ion	METHYL MERCURY ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MMC	3	Ligand/Ion	METHYL MERCURY ION

Sites (36, 36)

Asymmetric Unit (36, 36)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH C:262 , HOH C:264 , G C:1071	BINDING SITE FOR RESIDUE CD C 201
02	AC2	SOFTWARE	HOH C:445 , HOH C:446 , HOH C:447 , A C:1086 , G C:1087	BINDING SITE FOR RESIDUE CD C 202
03	AC3	SOFTWARE	HOH C:268 , HOH C:269 , HOH C:270 , A C:1073 , G C:1093 , U C:1094 , C C:1097	BINDING SITE FOR RESIDUE MG C 210
04	AC4	SOFTWARE	HOH C:254 , A C:1067 , HOH D:255 , HOH D:256 , A D:1095	BINDING SITE FOR RESIDUE CD C 211
05	AC5	SOFTWARE	LYS A:103 , GLU A:106 , GLU B:122 , C C:1076	BINDING SITE FOR RESIDUE MG A 214
06	AC6	SOFTWARE	HOH C:424 , HOH C:425 , U C:1061 , G C:1062 , G C:1063 , A C:1070	BINDING SITE FOR RESIDUE MG C 215
07	AC7	SOFTWARE	A C:1106	BINDING SITE FOR RESIDUE MG C 223
08	AC8	SOFTWARE	G C:1051	BINDING SITE FOR RESIDUE MG C 225
09	AC9	SOFTWARE	A C:1069 , A C:1070 , C C:1072 , A C:1073	BINDING SITE FOR RESIDUE MG C 226
10	BC1	SOFTWARE	A C:1084	BINDING SITE FOR RESIDUE MG C 228
11	BC2	SOFTWARE	HOH C:258 , HOH C:259 , HOH C:260 , HOH C:261 , A C:1070 , C C:1072	BINDING SITE FOR RESIDUE MG C 257
12	BC3	SOFTWARE	HOH C:274 , HOH C:275 , HOH C:276 , HOH C:277 , HOH C:278 , U C:1083	BINDING SITE FOR RESIDUE MG C 273
13	BC4	SOFTWARE	HOH D:460 , HOH D:461 , HOH D:462 , HOH D:463 , A D:1086 , G D:1087	BINDING SITE FOR RESIDUE CD D 302
14	BC5	SOFTWARE	A C:1095 , A D:1067	BINDING SITE FOR RESIDUE CD D 311
15	BC6	SOFTWARE	HOH D:305 , HOH D:391 , U D:1101	BINDING SITE FOR RESIDUE MG D 318
16	BC7	SOFTWARE	A D:1069 , A D:1070 , C D:1072 , A D:1073	BINDING SITE FOR RESIDUE MG D 326
17	BC8	SOFTWARE	HOH D:355 , HOH D:356 , HOH D:357 , HOH D:358 , G D:1051	BINDING SITE FOR RESIDUE MG D 354
18	BC9	SOFTWARE	HOH D:361 , HOH D:362 , HOH D:363 , HOH D:364 , G D:1107	BINDING SITE FOR RESIDUE MG D 360
19	CC1	SOFTWARE	HOH D:367 , HOH D:368	BINDING SITE FOR RESIDUE MG D 365
20	CC2	SOFTWARE	HOH D:377 , HOH D:378 , HOH D:379 , U D:1061 , G D:1062 , G D:1063 , A D:1070	BINDING SITE FOR RESIDUE MG D 375
21	CC3	SOFTWARE	HOH D:381 , HOH D:382 , HOH D:383 , HOH D:384 , A D:1070 , G D:1071 , C D:1072	BINDING SITE FOR RESIDUE MG D 380
22	CC4	SOFTWARE	HOH D:386 , HOH D:387 , HOH D:388 , HOH D:389 , A D:1073 , U D:1094	BINDING SITE FOR RESIDUE MG D 385
23	CC5	SOFTWARE	HOH D:392 , HOH D:394 , HOH D:396 , G D:1071	BINDING SITE FOR RESIDUE CD D 390
24	CC6	SOFTWARE	HOH D:399 , HOH D:400 , HOH D:401 , HOH D:402 , HOH D:403	BINDING SITE FOR RESIDUE MG D 397
25	CC7	SOFTWARE	MET A:113 , ALA A:118	BINDING SITE FOR RESIDUE CD A 413
26	CC8	SOFTWARE	THR A:72 , LYS A:112 , ASP A:115 , G C:1059 , U C:1060	BINDING SITE FOR RESIDUE CD A 414
27	CC9	SOFTWARE	HOH C:438 , HOH C:440 , HOH C:441 , HOH C:442 , HOH C:443 , G C:1054	BINDING SITE FOR RESIDUE MG C 437
28	DC1	SOFTWARE	A C:1077 , U C:1078 , G C:1089	BINDING SITE FOR RESIDUE MMC C 227
29	DC2	SOFTWARE	U C:1061 , A C:1069 , A C:1070	BINDING SITE FOR RESIDUE MMC C 230
30	DC3	SOFTWARE	U D:1061 , A D:1069 , A D:1070	BINDING SITE FOR RESIDUE MMC D 332
31	DC4	SOFTWARE	A D:1077 , U D:1078 , G D:1089	BINDING SITE FOR RESIDUE MMC D 347
32	DC5	SOFTWARE	THR A:19 , CYS A:39	BINDING SITE FOR RESIDUE MMC A 415
33	DC6	SOFTWARE	ALA A:18 , THR A:19 , VAL A:24 , ILE A:35 , CYS A:39	BINDING SITE FOR RESIDUE MMC A 416
34	DC7	SOFTWARE	HIS A:31 , C C:1097	BINDING SITE FOR RESIDUE MMC A 448
35	DC8	SOFTWARE	C D:1097	BINDING SITE FOR RESIDUE MMC D 451
36	TSR	AUTHOR	A C:1067 , A C:1095 , A D:1067 , A D:1095 , PRO A:22 , PRO A:23 , PRO A:26	PUTATIVE THIOSTREPTON/MICROCOCCIN BINDING SITE

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

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_THEMA	126-141	2	A:126-140 B:126-140

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_THEMA	126-141	1	A:126-140 -

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_THEMA	126-141	1	- B:126-140

Exons (0, 0)

(no "Exon" information available for 1MMS)

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
	(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 d1mmsa2 A:8-70 Ribosomal protein L11, N-terminal domain        d1mmsa1 A:71-140 Ribosomal protein L11, C-terminal domain              SCOP domains
               CATH domains 1mmsA01 A:8-71 Ribosomal protein L11, N-terminal domain         1mmsA02 A:72-140  [code=1.10.10.250, no name defined]                 CATH domains
               Pfam domains Ribosomal_L11_N-1mmsA01 A:8-66                             -------------------------------------------------------------------------- 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
                1mms A    8 QIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV  140
                                    17        27        37        47        57        67        77        87        97       107       117       127       137

Chain B from PDB  Type:PROTEIN  Length:70
 aligned with RL11_THEMA | P29395 from UniProtKB/Swiss-Prot  Length:141

    Alignment length:70
                                    80        90       100       110       120       130       140
          RL11_THEMA     71 KTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV  140
               SCOP domains d1mmsb_ B: Ribosomal protein L11, C-terminal domain                    SCOP domains
               CATH domains 1mmsB00 B:71-140  [code=1.10.10.250, no name defined]                  CATH domains
           Pfam domains (1) Ribosomal_L11-1mmsB01 B:71-139                                       - Pfam domains (1)
           Pfam domains (2) Ribosomal_L11-1mmsB02 B:71-139                                       - Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhh.............eeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------RIBOSOMAL_L11   PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                1mms B   71 KTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV  140
                                    80        90       100       110       120       130       140

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

Chain D from PDB  Type:RNA  Length:58
                                                                                           
                1mms D 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 (2, 3)

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)

Thermotoga maritima [TaxId: 2336] (1)

1a	d1mmsa1	A:71-140
1b	d1mmsb_	B:

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ribosomal L11/L12e N-terminal domain (53)

Superfamily: Ribosomal L11/L12e N-terminal domain (53)

Family: Ribosomal L11/L12e N-terminal domain (53)

Protein domain: Ribosomal protein L11, N-terminal domain (52)

Thermotoga maritima [TaxId: 2336] (2)

d1mmsa2

A:8-70

CATH Domains (2, 3)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Ribosomal protein L11, N-terminal domain (16)

Homologous Superfamily: Ribosomal protein L11, N-terminal domain (16)

[unclassified] (1)

1mmsA01

A:8-71

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)

2a	1mmsB00	B:71-140
2b	1mmsA02	A:72-140

Pfam Domains (2, 3)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Ribosomal_L11 (35)

Thermotoga maritima (3)

1a	Ribosomal_L11-1mmsB01	B:71-139
1b	Ribosomal_L11-1mmsB02	B:71-139

Clan: no clan defined [family: Ribosomal_L11_N] (8)

Family: Ribosomal_L11_N (8)

Thermotoga maritima (3)

Ribosomal_L11_N-1mmsA01

A:8-66

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

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	RL11_THEMA \| P29395
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	RL11_THEMA \| P29395	:	1eg0 1ip8 1jqm 1jqs 1jqt 1mvr 1oln 1pn7 1pn8 1r2w 1r2x 2bcw 2gky 2gkz 2jq7 2k3f 487d

Related Entries Specified in the PDB File

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