3V7E - JenaLib

Title :   CRYSTAL STRUCTURE OF YBXF BOUND TO THE SAM-I RIBOSWITCH APTAMER

Authors :   N. J. Baird, J. Zhang, T. Hamma, A. R. Ferre-D'Amare

Date :   21 Dec 11 (Deposition) - 07 Mar 12 (Release) - 18 Apr 12 (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 :   Rna-Protein Complex, Riboswitch, K-Turn, L7Ae-Like, A Member Of The L7Ae/L30E Superfamily, Unknown Function, K-Turn Motif, Ribosomal Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. J. Baird, J. Zhang, T. Hamma, A. R. Ferre-D'Amare
Ybxf And Ylxq Are Bacterial Homologs Of L7Ae And Bind K-Turns But Not K-Loops.
Rna V. 18 759 2012
PubMed-ID: 22355167 | Reference-DOI: 10.1261/RNA.031518.111

Compounds

Molecule 1 - RIBOSOME-ASSOCIATED PROTEIN L7AE-LIKE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BSU01090, RPLGB, YBAB, YBXF
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

Molecule 2 - SAM-I RIBOSWITCH APTAMER WITH AN ENGINEERED HELIX P3
	Chains	:	C, D
	Engineered	:	YES
	Organism Scientific	:	CALDANAEROBACTER SUBTERRANEUS SUBSP. TENGCONGENSIS
	Organism Taxid	:	119072
	Other Details	:	RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 42)

Sites (38, 38)

Asymmetric Unit (38, 38)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	U C:4 , U C:5 , A C:6 , A C:119 , U C:120 , G C:121 , A C:122	BINDING SITE FOR RESIDUE NCO C 901
02	AC2	SOFTWARE	G C:23 , C C:25 , U C:26 , G C:27 , G C:28	BINDING SITE FOR RESIDUE NCO C 902
03	AC3	SOFTWARE	C C:59 , G C:60 , U C:61 , G C:73 , A C:74 , NCO C:909	BINDING SITE FOR RESIDUE NCO C 903
04	AC4	SOFTWARE	A C:45 , A C:46 , G C:87 , G C:88	BINDING SITE FOR RESIDUE NCO C 904
05	AC5	SOFTWARE	A C:10 , G C:11 , A C:12 , A C:94 , U C:95 , U C:96	BINDING SITE FOR RESIDUE NCO C 905
06	AC6	SOFTWARE	U C:113 , G C:114 , A C:115	BINDING SITE FOR RESIDUE NCO C 906
07	AC7	SOFTWARE	A C:24 , C C:25 , U C:96 , C C:98 , U C:99 , G C:100 , A C:116 , A C:117	BINDING SITE FOR RESIDUE NCO C 907
08	AC8	SOFTWARE	C C:41 , G C:42 , G C:43	BINDING SITE FOR RESIDUE NCO C 908
09	AC9	SOFTWARE	C C:59 , NCO C:903	BINDING SITE FOR RESIDUE NCO C 909
10	BC1	SOFTWARE	A C:46 , A C:84 , G C:85	BINDING SITE FOR RESIDUE NCO C 910
11	BC2	SOFTWARE	G C:53 , U C:54 , A C:79 , G C:80 , G C:81	BINDING SITE FOR RESIDUE NCO C 911
12	BC3	SOFTWARE	C C:62 , A C:63 , G C:64	BINDING SITE FOR RESIDUE NCO C 912
13	BC4	SOFTWARE	U C:7 , G C:11 , A C:45 , C C:47 , U C:89 , G C:90 , U C:120 , G C:121	BINDING SITE FOR RESIDUE SAM C 913
14	BC5	SOFTWARE	G C:13 , G C:42 , C C:92 , HOH C:1007	BINDING SITE FOR RESIDUE MG C 914
15	BC6	SOFTWARE	A C:36	BINDING SITE FOR RESIDUE MG C 917
16	BC7	SOFTWARE	G C:100 , C C:101 , A C:102	BINDING SITE FOR RESIDUE MG C 918
17	BC8	SOFTWARE	G C:1 , HOH C:1003 , HOH D:501 , HOH D:502	BINDING SITE FOR RESIDUE MG C 919
18	BC9	SOFTWARE	G C:19	BINDING SITE FOR RESIDUE MG C 920
19	CC1	SOFTWARE	U C:83 , A C:84	BINDING SITE FOR RESIDUE MG C 921
20	CC2	SOFTWARE	C C:104 , G C:105	BINDING SITE FOR RESIDUE MG C 922
21	CC3	SOFTWARE	HOH C:1001 , HOH C:1004 , HOH C:1005	BINDING SITE FOR RESIDUE MG C 923
22	CC4	SOFTWARE	G C:18 , G C:19 , G C:35 , HOH C:1002	BINDING SITE FOR RESIDUE MG C 924
23	CC5	SOFTWARE	C C:3 , HOH C:1006	BINDING SITE FOR RESIDUE MG C 926
24	CC6	SOFTWARE	U D:204 , U D:205 , A D:319 , U D:320 , G D:321	BINDING SITE FOR RESIDUE NCO D 401
25	CC7	SOFTWARE	A D:210 , G D:211 , A D:294 , U D:295 , U D:296	BINDING SITE FOR RESIDUE NCO D 402
26	CC8	SOFTWARE	A D:245 , A D:246 , U D:286 , G D:287 , G D:288 , U D:289	BINDING SITE FOR RESIDUE NCO D 403
27	CC9	SOFTWARE	G D:223 , C D:225 , U D:226 , G D:227 , G D:228 , C D:229 , HOH D:502	BINDING SITE FOR RESIDUE NCO D 404
28	DC1	SOFTWARE	U D:313 , G D:314 , A D:315	BINDING SITE FOR RESIDUE NCO D 405
29	DC2	SOFTWARE	C D:259 , G D:260 , U D:261 , G D:273	BINDING SITE FOR RESIDUE NCO D 406
30	DC3	SOFTWARE	U D:207 , C D:208 , G D:211 , A D:245 , A D:246 , C D:247 , U D:289 , G D:290 , C D:291 , U D:320 , G D:321	BINDING SITE FOR RESIDUE SAM D 407
31	DC4	SOFTWARE	U D:299 , G D:300 , HOH D:506 , HOH D:507	BINDING SITE FOR RESIDUE MG D 408
32	DC5	SOFTWARE	G D:201	BINDING SITE FOR RESIDUE MG D 409
33	DC6	SOFTWARE	G D:300	BINDING SITE FOR RESIDUE MG D 410
34	DC7	SOFTWARE	G D:213 , G D:242	BINDING SITE FOR RESIDUE MG D 412
35	DC8	SOFTWARE	C D:203 , C D:324	BINDING SITE FOR RESIDUE MG D 413
36	DC9	SOFTWARE	HOH D:503 , HOH D:504	BINDING SITE FOR RESIDUE MG D 414
37	EC1	SOFTWARE	U D:217 , G D:218 , HOH D:505	BINDING SITE FOR RESIDUE MG D 415
38	EC2	SOFTWARE	A D:316	BINDING SITE FOR RESIDUE MG D 416

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:81
 aligned with RXL7_BACSU | P46350 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:81
                                    11        21        31        41        51        61        71        81 
           RXL7_BACSU     2 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSMVESMKKLGKACGIEVGAAAVAIIL  82
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.eeeehhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhh..eeee.hhhhhhhhh.......eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3v7e A 502 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSMVESMKKLGKACGIEVGAAAVAIIL 582
                                   511       521       531       541       551       561       571       581

Chain B from PDB  Type:PROTEIN  Length:77
 aligned with RXL7_BACSU | P46350 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:77
                                    11        21        31        41        51        61        71       
           RXL7_BACSU     2 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSMVESMKKLGKACGIEVGAAAV  78
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.......hhhhhhhhh......ee..............hhhhhh...ee......hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 3v7e B 602 SYDKVSQAKSIIIGTKQTVKALKRGSVKEVVVAKDADPILTSSVVSLAEDQGISVSMVESMKKLGKACGIEVGAAAV 678
                                   611       621       631       641       651       661       671

Chain C from PDB  Type:RNA  Length:126
                                                                                                                                                              
                 3v7e C   1 GGCUUAUCAAGAGAGGUGGAGGGACUGGCCCGAUGAAACCCGGCAACCACUAGUCUAGCGUCAGCUUCGGCUGACGCUAGGCUAGUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCA 126
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain D from PDB  Type:RNA  Length:126
                                                                                                                                                              
                 3v7e D 201 GGCUUAUCAAGAGAGGUGGAGGGACUGGCCCGAUGAAACCCGGCAACCACUAGUCUAGCGUCAGCUUCGGCUGACGCUAGGCUAGUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCA 326
                                   210       220       230       240       250       260       270       280       290       300       310       320

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 (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RXL7_BACSU | P46350)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	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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