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Title :   CO-CRYSTAL STRUCTURE OF A BACTERIAL C-DI-GMP RIBOSWITCH

Authors :   N. Kulshina, N. J. Baird, A. R. Ferre-D'Amare

Date :   02 Sep 09 (Deposition) - 10 Nov 09 (Release) - 22 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

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

Keywords :   Riboswitch, Rna, U1A, Rna/Rna Binding Protein Complex, Acetylation, Mrna Processing, Mrna Splicing, Nucleus, Phosphoprotein, Ribonucleoprotein, Rna-Binding, Spliceosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Kulshina, N. J. Baird, A. R. Ferre-D'Amare
Recognition Of The Bacterial Second Messenger Cyclic Diguanylate By Its Cognate Riboswitch.
Nat. Struct. Mol. Biol. V. 16 1212 2009
PubMed-ID: 19898478 | Reference-DOI: 10.1038/NSMB.1701
(for further references see the PDB file header)

Molecule 1 - C-DI-GMP RIBOSWITCH
	Chains	:	A, B
	Engineered	:	YES
	Other Details	:	IN VITRO TRANSCRIPTION
	Synthetic	:	YES

Molecule 2 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 6-96, RRM 1 DOMAIN
	Gene	:	SNRPA, U1A
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	U1 SNRNP PROTEIN A, U1A PROTEIN, U1-A

		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)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	C2E	2	Ligand/Ion	9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	C2E	1	Ligand/Ion	9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	C2E	1	Ligand/Ion	9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	G A:4 , C A:5 , A A:8 , G A:9 , G A:10 , G A:11 , C A:36 , A A:37 , A A:38 , A A:39 , G A:40 , C A:87 , C A:88	BINDING SITE FOR RESIDUE C2E A 501
2	AC2	SOFTWARE	G B:104 , C B:105 , C B:107 , A B:108 , G B:109 , G B:110 , G B:111 , C B:136 , A B:137 , A B:138 , C B:187 , C B:188	BINDING SITE FOR RESIDUE C2E B 601

(no "SS Bond" information available for 3IWN)

(no "Cis Peptide Bond" information available for 3IWN)

(no "SAP(SNP)/Variant" information available for 3IWN)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	SNRPA_HUMAN	10-89 208-282	2	C:805-884 D:905-984 -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	SNRPA_HUMAN	10-89 208-282	1	C:805-884 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	SNRPA_HUMAN	10-89 208-282	1	- D:905-984 -

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000243563	1	ENSE00001052136	chr19:41256779-41257386	608	SNRPA_HUMAN	1-25	25	2	C:801-820 D:901-920	20 20
1.2	ENST00000243563	2	ENSE00000707951	chr19:41263237-41263409	173	SNRPA_HUMAN	25-82	58	2	C:820-877 D:920-977	58 58
1.3	ENST00000243563	3	ENSE00000707956	chr19:41265336-41265515	180	SNRPA_HUMAN	83-142	60	2	C:878-891 D:978-991	14 14
1.4	ENST00000243563	4	ENSE00000707961	chr19:41268806-41268979	174	SNRPA_HUMAN	143-200	58	0	-	-
1.5	ENST00000243563	5	ENSE00000842333	chr19:41269492-41269580	89	SNRPA_HUMAN	201-230	30	0	-	-
1.6	ENST00000243563	6	ENSE00000842334	chr19:41270913-41271290	378	SNRPA_HUMAN	230-282	53	0	-	-

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:RNA  Length:93
                                                                                                                             
                 3iwn A   1 CACGCACAGGGCAAACCAUUCGAAAGAGUGGGACGCAAAGCCUCCGGCCUAAACGGCAUUGCACUCCGCCGUAGGUAGCGGGGUUACCGAUGG  93
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:RNA  Length:93
                                                                                                                             
                 3iwn B 101 CACGCACAGGGCAAACCAUUCGAAAGAGUGGGACGCAAAGCCUCCGGCCUAAACGGCAUUGCACUCCGCCGUAGGUAGCGGGGUUACCGAUGG 193
                                   110       120       130       140       150       160       170       180       190

Chain C from PDB  Type:PROTEIN  Length:91
 aligned with SNRPA_HUMAN | P09012 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:91
                                    15        25        35        45        55        65        75        85        95 
          SNRPA_HUMAN     6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK  96
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3iwnC00 C:801-891  [code=3.30.70.330, no name defined]                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhh.eeeee.........eeeeee.hhhhhhhhhhhh...ee..ee.eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RRM  PDB: C:805-884 UniProt: 10-89                                              ------- PROSITE
           Transcript 1 (1) Exon 1.1            ---------------------------------------------------------Exon 1.3       Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: C:820-877 UniProt: 25-82                   -------------- Transcript 1 (2)
                 3iwn C 801 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 891
                                   810       820       830       840       850       860       870       880       890

Chain D from PDB  Type:PROTEIN  Length:91
 aligned with SNRPA_HUMAN | P09012 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:91
                                    15        25        35        45        55        65        75        85        95 
          SNRPA_HUMAN     6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK  96
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3iwnD00 D:901-991  [code=3.30.70.330, no name defined]                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.......hhhhhhhhhhhhhhhhh.eeeee...hhhhh..eeeee.hhhhhhhhhhhhh..ee..ee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RRM  PDB: D:905-984 UniProt: 10-89                                              ------- PROSITE
           Transcript 1 (1) Exon 1.1            ---------------------------------------------------------Exon 1.3       Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: D:920-977 UniProt: 25-82                   -------------- Transcript 1 (2)
                 3iwn D 901 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 991
                                   910       920       930       940       950       960       970       980       990

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 '\|'

(no "SCOP Domain" information available for 3IWN)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.330, no name defined] (307)

[unclassified] (45)

1a	3iwnC00	C:801-891
1b	3iwnD00	D:901-991

(no "Pfam Domain" information available for 3IWN)

Asymmetric Unit(hide GO term definitions)

Chain C,D (SNRPA_HUMAN | P09012)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0030619	U1 snRNA binding	Interacting selectively and non-covalently with the U1 small nuclear RNA (U1 snRNA).
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0017069	snRNA binding	Interacting selectively and non-covalently with a small nuclear RNA (snRNA).
	GO:0035614	snRNA stem-loop binding	Interacting selectively and non-covalently with a stem-loop in a small nuclear RNA (snRNA). An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop.
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
cellular component
	GO:0005685	U1 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U1.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005681	spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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Description

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Ligands, Modified Residues, Ions (1, 2)

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