3U4M - JenaLib

Title :   CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN TTHL1 IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS

Authors :   A. G. Gabdulkhakov, N. A. Nevskaya, S. V. Nikonov

Date :   10 Oct 11 (Deposition) - 08 Aug 12 (Release) - 23 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   S. Tishchenko, A. Gabdulkhakov, N. Nevskaya, A. Sarskikh, O. Kostareva, E. Nikonova, A. Sycheva, S. Moshkovskii, M. Garber, S. Nikonov
High-Resolution Crystal Structure Of The Isolated Ribosomal L1 Stalk.
Acta Crystallogr. , Sect. D V. 68 1051 2012
PubMed-ID: 22868771 | Reference-DOI: 10.1107/S0907444912020136

Compounds

Molecule 1 - 50S RIBOSOMAL PROTEIN L1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A-PL/TTHL1
	Expression System Strain	:	BL11(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RPLA, RPL1
	Mutation	:	YES
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

Molecule 2 - RNA (80-MER)
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC18/RRNATTH
	Expression System Strain	:	BL11(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Other Details	:	FRAGMENT OF 23S RRNA

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 21)

Sites (21, 21)

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:197 , THR A:207 , PHE A:208 , LEU A:209	BINDING SITE FOR RESIDUE SO4 A 301
02	AC2	SOFTWARE	ALA A:33 , ALA A:35 , PHE A:37 , ASP A:38 , GLU A:39 , ILE A:83 , LYS A:84 , GLU A:87 , ALA A:178 , SER A:179 , MG A:305 , HOH A:417	BINDING SITE FOR RESIDUE MLI A 302
03	AC3	SOFTWARE	ALA A:112 , ILE A:156 , ARG A:160 , ILE A:161 , GLU A:162 , HOH A:453 , HOH A:457	BINDING SITE FOR RESIDUE MLI A 303
04	AC4	SOFTWARE	PHE A:37 , ASP A:38 , ALA A:78 , GLY A:80 , GLY A:96 , GLU A:97 , GLU A:98 , HOH A:474	BINDING SITE FOR RESIDUE MLI A 304
05	AC5	SOFTWARE	ALA A:33 , ALA A:35 , PHE A:37 , GLU A:39 , MLI A:302	BINDING SITE FOR RESIDUE MG A 305
06	AC6	SOFTWARE	GLU A:81	BINDING SITE FOR RESIDUE CL A 306
07	AC7	SOFTWARE	GLY A:60 , THR A:61 , HIS A:199	BINDING SITE FOR RESIDUE CL A 307
08	AC8	SOFTWARE	ARG A:6 , LEU A:10 , THR A:34 , HOH A:408 , HOH A:409	BINDING SITE FOR RESIDUE NA A 308
09	AC9	SOFTWARE	ARG A:6 , LEU A:10 , LEU A:32 , ALA A:33 , THR A:34 , GLU A:39 , MET A:218 , GLY A:219	BINDING SITE FOR RESIDUE NA A 309
10	BC1	SOFTWARE	ARG A:6 , HOH A:466 , C B:2129 , U B:2130	BINDING SITE FOR RESIDUE NA A 310
11	BC2	SOFTWARE	GLU A:42 , THR A:216 , THR A:217 , G B:2123 , C B:2175 , A B:2176	BINDING SITE FOR RESIDUE NA A 311
12	BC3	SOFTWARE	C B:2175 , A B:2176 , HOH B:2304 , HOH B:2321 , HOH B:2372 , HOH B:2375 , HOH B:2376 , HOH B:2383 , HOH B:2388	BINDING SITE FOR RESIDUE SO4 B 2201
13	BC4	SOFTWARE	A B:2134 , A B:2135 , G B:2156 , G B:2157	BINDING SITE FOR RESIDUE MLI B 2202
14	BC5	SOFTWARE	C B:2178 , C B:2179 , HOH B:2361 , HOH B:2362 , HOH B:2370 , HOH B:2391	BINDING SITE FOR RESIDUE MLI B 2203
15	BC6	SOFTWARE	U B:2130 , G B:2131 , C B:2139 , C B:2140 , G B:2152 , G B:2159 , HOH B:2371	BINDING SITE FOR RESIDUE MLI B 2204
16	BC7	SOFTWARE	A B:2119 , G B:2121 , A B:2170 , HOH B:2325 , HOH B:2334 , HOH B:2400 , HOH B:2410 , HOH B:2414 , HOH B:2416	BINDING SITE FOR RESIDUE MLI B 2205
17	BC8	SOFTWARE	U B:2122 , G B:2123 , HOH B:2302 , HOH B:2321 , HOH B:2325 , HOH B:2326	BINDING SITE FOR RESIDUE MG B 2206
18	BC9	SOFTWARE	HOH B:2304 , HOH B:2315 , HOH B:2321 , HOH B:2325 , HOH B:2363 , HOH B:2399	BINDING SITE FOR RESIDUE MG B 2207
19	CC1	SOFTWARE	G B:2120 , HOH B:2304 , HOH B:2376 , HOH B:2377 , HOH B:2378 , HOH B:2424	BINDING SITE FOR RESIDUE MG B 2208
20	CC2	SOFTWARE	U B:2172 , HOH B:2341 , HOH B:2379 , HOH B:2380 , HOH B:2381	BINDING SITE FOR RESIDUE MG B 2209
21	CC3	SOFTWARE	GLU A:42 , HIS A:44 , G B:2123 , G B:2124	BINDING SITE FOR RESIDUE NA B 2210

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
	(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:228
 aligned with RL1_THETH | P27150 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
           RL1_THETH      2 PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS  229
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh........hhhhhhhhhh.........eeeeeeee.....hhhhh.eeeee..........eeeee..hhhhhhhhh...eeee..hhhhhhhh.....eeee...hhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhh.eeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhh.........eeeeeeee....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L1        ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3u4m A    1 PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS  228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:RNA  Length:80
                                                                                                                 
                3u4m B 2105 GGGAUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUUCCC 2184
                                  2114      2124      2134      2144      2154      2164      2174      2184

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RL1_THETH | P27150)

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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