3HHN - JenaLib

Title :   CRYSTAL STRUCTURE OF CLASS I LIGASE RIBOZYME SELF-LIGATION PRODUCT, IN COMPLEX WITH U1A RBD

Authors :   D. M. Shechner, R. A. Grant, S. C. Bagby, D. P. Bartel

Date :   15 May 09 (Deposition) - 24 Nov 09 (Release) - 12 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.99

Chains :   Asym./Biol. Unit : B,C,D,E

Keywords :   Ligase Ribozyme, Ribozyme, Catalytic Rna, Protein-Rna Complex, Ribonucleoprotein, Rna-Binding, Ligase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Shechner, R. A. Grant, S. C. Bagby, Y. Koldobskaya, J. A. Piccirilli, D. P. Bartel
Crystal Structure Of The Catalytic Core Of An Rna-Polymerase Ribozyme.
Science V. 326 1271 2009
PubMed-ID: 19965478 | Reference-DOI: 10.1126/SCIENCE.1174676
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 36)

Sites (34, 34)

Asymmetric Unit (34, 34)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH B:183 , HOH B:185 , HOH B:186 , HOH B:187 , HOH B:188 , HOH B:189	BINDING SITE FOR RESIDUE MG B 184
02	AC2	SOFTWARE	A C:31 , A C:32 , HOH C:1027 , HOH C:1028 , HOH C:1029 , HOH C:1030	BINDING SITE FOR RESIDUE MG C 1019
03	AC3	SOFTWARE	HOH C:1031 , HOH C:1032 , HOH C:1033 , HOH C:1034 , HOH C:1035 , HOH C:1036	BINDING SITE FOR RESIDUE MG C 1020
04	AC4	SOFTWARE	C C:70 , G C:72 , U C:106 , HOH C:1037 , HOH C:1038 , HOH C:1039 , HOH C:1040	BINDING SITE FOR RESIDUE MG C 1021
05	AC5	SOFTWARE	G C:77 , HOH C:1041 , HOH C:1042 , HOH C:1043 , HOH C:1044 , HOH C:1045	BINDING SITE FOR RESIDUE MG C 1022
06	AC6	SOFTWARE	A C:4 , A C:115 , HOH C:1046 , HOH C:1047 , HOH C:1048 , HOH C:1049 , HOH C:1050	BINDING SITE FOR RESIDUE MG C 1023
07	AC7	SOFTWARE	HOH C:59 , HOH C:61 , HOH C:62 , HOH C:63 , HOH C:64 , HOH C:65	BINDING SITE FOR RESIDUE MG C 60
08	AC8	SOFTWARE	HOH C:1051 , HOH C:1052 , HOH C:1053 , HOH C:1054 , HOH C:1055 , HOH C:1056	BINDING SITE FOR RESIDUE MG C 1024
09	AC9	SOFTWARE	HOH C:1057 , HOH C:1058 , HOH C:1059 , HOH C:1060 , HOH C:1061 , HOH C:1062	BINDING SITE FOR RESIDUE MG C 1025
10	BC1	SOFTWARE	HOH C:1063 , HOH C:1064 , HOH C:1065 , HOH C:1066 , HOH C:1067 , HOH C:1068	BINDING SITE FOR RESIDUE MG C 1026
11	BC2	SOFTWARE	HOH C:122 , HOH C:124 , HOH C:125 , HOH C:126 , HOH C:127 , HOH C:128	BINDING SITE FOR RESIDUE MG C 123
12	BC3	SOFTWARE	HOH C:136 , HOH C:138 , HOH C:139 , HOH C:140 , HOH C:141 , HOH C:142	BINDING SITE FOR RESIDUE MG C 137
13	BC4	SOFTWARE	HOH C:143 , HOH C:145 , HOH C:146 , HOH C:147 , HOH C:148 , HOH C:149	BINDING SITE FOR RESIDUE MG C 144
14	BC5	SOFTWARE	HOH C:150 , HOH C:152 , HOH C:153 , HOH C:154 , HOH C:155 , HOH C:156	BINDING SITE FOR RESIDUE MG C 151
15	BC6	SOFTWARE	C C:47 , HOH C:157 , HOH C:159 , HOH C:160 , HOH C:161 , HOH C:162	BINDING SITE FOR RESIDUE MG C 158
16	BC7	SOFTWARE	HOH C:163 , HOH C:165 , HOH C:166 , HOH C:167 , HOH C:168 , C C:1009	BINDING SITE FOR RESIDUE MG C 164
17	BC8	SOFTWARE	HOH C:169 , HOH C:171 , HOH C:172 , HOH C:173 , HOH C:174 , HOH C:175	BINDING SITE FOR RESIDUE MG C 170
18	BC9	SOFTWARE	HOH C:176 , HOH C:178 , HOH C:179 , HOH C:180 , HOH C:181 , HOH C:182	BINDING SITE FOR RESIDUE MG C 177
19	CC1	SOFTWARE	HOH C:197 , HOH C:199 , HOH C:200 , HOH C:201 , HOH C:202 , G C:1008	BINDING SITE FOR RESIDUE MG C 198
20	CC2	SOFTWARE	C C:47 , G C:74	BINDING SITE FOR RESIDUE MG C 204
21	CC3	SOFTWARE	A C:31	BINDING SITE FOR RESIDUE MG C 222
22	CC4	SOFTWARE	A E:31 , A E:32 , HOH E:1029 , HOH E:1030 , HOH E:1031 , HOH E:1032	BINDING SITE FOR RESIDUE MG E 1019
23	CC5	SOFTWARE	HOH E:1033 , HOH E:1034 , HOH E:1035 , HOH E:1036 , HOH E:1037 , HOH E:1038	BINDING SITE FOR RESIDUE MG E 1020
24	CC6	SOFTWARE	G E:69 , C E:70 , U E:106 , HOH E:1039 , HOH E:1040 , HOH E:1041 , HOH E:1042	BINDING SITE FOR RESIDUE MG E 1021
25	CC7	SOFTWARE	G E:77 , HOH E:1043 , HOH E:1044 , HOH E:1045 , HOH E:1046 , HOH E:1047	BINDING SITE FOR RESIDUE MG E 1022
26	CC8	SOFTWARE	HOH E:58 , A E:115 , HOH E:1048 , HOH E:1049 , HOH E:1050 , HOH E:1051	BINDING SITE FOR RESIDUE MG E 1023
27	CC9	SOFTWARE	HOH E:66 , HOH E:1052 , HOH E:1053 , HOH E:1054 , HOH E:1055 , HOH E:1056	BINDING SITE FOR RESIDUE MG E 1024
28	DC1	SOFTWARE	HOH E:1057 , HOH E:1058 , HOH E:1059 , HOH E:1060 , HOH E:1061 , HOH E:1062	BINDING SITE FOR RESIDUE MG E 1025
29	DC2	SOFTWARE	HOH E:1063 , HOH E:1064 , HOH E:1065 , HOH E:1066 , HOH E:1067 , HOH E:1068	BINDING SITE FOR RESIDUE MG E 1026
30	DC3	SOFTWARE	HOH E:1069 , HOH E:1070 , HOH E:1071 , HOH E:1072 , HOH E:1073 , HOH E:1074	BINDING SITE FOR RESIDUE MG E 1027
31	DC4	SOFTWARE	HOH E:1075 , HOH E:1076 , HOH E:1077 , HOH E:1078 , HOH E:1079 , HOH E:1080	BINDING SITE FOR RESIDUE MG E 1028
32	DC5	SOFTWARE	HOH E:129 , HOH E:131 , HOH E:132 , HOH E:133 , HOH E:134 , HOH E:135	BINDING SITE FOR RESIDUE MG E 130
33	DC6	SOFTWARE	HOH E:190 , HOH E:192 , HOH E:193 , HOH E:194 , HOH E:195 , HOH E:196	BINDING SITE FOR RESIDUE MG E 191
34	DC7	SOFTWARE	A E:4 , A E:6	BINDING SITE FOR RESIDUE MG E 203

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (3, 6)

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 B from PDB  Type:PROTEIN  Length:92
 aligned with SNRPA_HUMAN | P09012 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:92
                                    16        26        36        46        56        66        76        86        96  
         SNRPA_HUMAN      7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK   98
               SCOP domains d3hhnb_ B: Splicesomal U1A protein                                                           SCOP domains
               CATH domains 3hhnB00 B:7-98  [code=3.30.70.330, no name defined]                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee......hhhhhhhhhhhhhhhhh.eeeee..........eeeee.hhhhhhhhhhhhh.........eeee....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---RRM  PDB: B:10-89 UniProt: 10-89                                                --------- PROSITE
           Transcript 1 (1) Exon 1.1           ---------------------------------------------------------Exon 1.3         Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.2  PDB: B:25-82 UniProt: 25-82                     ---------------- Transcript 1 (2)
                3hhn B    7 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK   98
                                    16        26        36        46        56        66        76        86        96

Chain C from PDB  Type:RNA  Length:137
                                                                                                                                                                          
                3hhn C   -7 UCCAGUAGGAACACUAUACUACUGGAUAAUCAAAGACAAAUCUGCCCGAAGGGCUUGAGAACAUACCCAUUGCACUCCGGGUAUGCAGAGGUGGCAGCCUCCGGUGGGUUAAAACCCAACGUUCUCAACAAUAGUGa  121
                                  || 3        13        23        33        43        53   || 1006      1016 ||     74        84        94       104       114      |
                                 -1|                                                      57|             1018|                                                   121-A23
                                   1                                                     1001                67

Chain D from PDB  Type:PROTEIN  Length:93
 aligned with SNRPA_HUMAN | P09012 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:93
                                    15        25        35        45        55        65        75        85        95   
         SNRPA_HUMAN      6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK   98
               SCOP domains d3hhnd_ D: Splicesomal U1A protein                                                            SCOP domains
               CATH domains 3hhnD00 D:6-98  [code=3.30.70.330, no name defined]                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhh.eeeee..........eeeee.hhhhhhhhhhhhh.........eeee....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RRM  PDB: D:10-89 UniProt: 10-89                                                --------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: D:6-2---------------------------------------------------------Exon 1.3         Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: D:25-82 UniProt: 25-82                     ---------------- Transcript 1 (2)
                3hhn D    6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK   98
                                    15        25        35        45        55        65        75        85        95

Chain E from PDB  Type:RNA  Length:137
                                                                                                                                                                          
                3hhn E   -7 UCCAGUAGGAACACUAUACUACUGGAUAAUCAAAGACAAAUCUGCCCGAAGGGCUUGAGAACAUACCCAUUGCACUCCGGGUAUGCAGAGGUGGCAGCCUCCGGUGGGUUAAAACCCAACGUUCUCAACAAUAGUGa  121
                                  || 3        13        23        33        43        53   || 1006      1016 ||     74        84        94       104       114      |
                                 -1|                                                      57|             1018|                                                   121-A23
                                   1                                                     1001                67

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)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

Chain B,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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	3hhn
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