1U6B | PR0133 - JenaLib

Molecule 1 - 197-MER
	Chains	:	B
	Engineered	:	YES
	Fragment	:	GROUP I INTRON
	Other Details	:	RNA WAS IS TRANSCRIBED BY T7 RNA POLYMERASE.
	Synthetic	:	YES

*Molecule 2 - 5'-R(APAPGPCPCPAPCPAPCPAPAPAPCPCPAPGPAPCP GP GPCPC)-3'*
	Chains	:	C
	Engineered	:	YES
	Fragment	:	GROUP I EXON
	Synthetic	:	YES

*Molecule 3 - 5'-R(CPAP(5MU))-3'**
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 4 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SNRPA
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	U1 SNRNP PROTEIN A, U1A PROTEIN, U1-A

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 21)

Sites (16, 16)

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	A B:87 , A B:127 , G B:128 , A B:172 , HOH B:1030 , HOH C:101	BINDING SITE FOR RESIDUE K B 2
02	AC2	SOFTWARE	A B:149 , A B:150 , G B:151 , G B:152	BINDING SITE FOR RESIDUE K B 4
03	AC3	SOFTWARE	U B:124 , U B:126 , A B:127 , C B:171	BINDING SITE FOR RESIDUE K B 1015
04	AC4	SOFTWARE	U B:9 , G B:10 , A C:1 , 5MU D:1 , A D:2	BINDING SITE FOR RESIDUE K B 1016
05	AC5	SOFTWARE	G B:23 , G B:24	BINDING SITE FOR RESIDUE K B 1017
06	AC6	SOFTWARE	C B:88 , G B:170 , A B:172 , A C:1 , 5MU D:1	BINDING SITE FOR RESIDUE MG B 1018
07	AC7	SOFTWARE	A B:172 , U B:173 , A B:174	BINDING SITE FOR RESIDUE MG B 3
08	AC8	SOFTWARE	G B:125 , U B:126	BINDING SITE FOR RESIDUE MG B 1019
09	AC9	SOFTWARE	HOH B:1071	BINDING SITE FOR RESIDUE MG B 1020
10	BC1	SOFTWARE	U B:124 , C B:171	BINDING SITE FOR RESIDUE MG B 1023
11	BC2	SOFTWARE	G B:37 , G B:38 , A B:39	BINDING SITE FOR RESIDUE MG B 1024
12	BC3	SOFTWARE	A B:48 , U B:133 , HOH B:1054	BINDING SITE FOR RESIDUE MG B 1025
13	BC4	SOFTWARE	C B:73 , C B:74	BINDING SITE FOR RESIDUE MG B 1026
14	BC5	SOFTWARE	U B:51 , G B:125 , HOH B:1061 , HOH B:1073	BINDING SITE FOR RESIDUE MG B 1027
15	BC6	SOFTWARE	G B:181 , G B:182	BINDING SITE FOR RESIDUE MG B 1028
16	BC7	SOFTWARE	U B:15 , C B:29 , HOH B:1074	BINDING SITE FOR RESIDUE MG B 1029

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (3, 3)

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
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Chain A from PDB  Type:PROTEIN  Length:95
 aligned with SNRPA_HUMAN | P09012 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:95
                                    13        23        33        43        53        63        73        83        93     
         SNRPA_HUMAN      4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK   98
               SCOP domains d1u6ba_ A: Splicesomal U1A protein                                                              SCOP domains
               CATH domains 1u6bA00 A:4-98  [code=3.30.70.330, no name defined]                                             CATH domains
               Pfam domains --------RRM_1-1u6bA01 A:12-83                                                   --------------- Pfam domains
         Sec.struct. author .......eeeee......hhhhhhhhhhh.......eeeeee.........eeeee.hhhhhhhhhhhh...ee..ee.eeee....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------RRM  PDB: A:10-89 UniProt: 10-89                                                --------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:4-25 ---------------------------------------------------------Exon 1.3         Transcript 1 (1)
           Transcript 1 (2) ---------------------Exon 1.2  PDB: A:25-82 UniProt: 25-82                     ---------------- Transcript 1 (2)
                1u6b A    4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK   98
                                    13        23        33        43        53        63        73        83        93

Chain B from PDB  Type:RNA  Length:197
                                                                                                                                                                                                                                      
                1u6b B    1 gGCCGUGUGCCUUGCGCCGGGAAACCACGCAAGGGAUGGUGUCAAAUUCGGCGAAACCUAAGCGCCCGCCCGGGCGUAUGGCAACGCCGAGCCAAGCUUCGCAGCCAUUGCACUCCGGCUGCGAUGAAGGUGUAGAGACUAGACGGCACCCACCUAAGGCAAACGCUAUGGUGAAGGCAUAGUCCAGGGAGUGGCGa  190
                            ||      13        23        33        43        53        63        73        83        93       103   || 1006       113       123       133       143       153       163       173       183      |
                            1-GTP                                                                                                107|         1014|                                                                           190-A23
                             5                                                                                                   1001           112

Chain C from PDB  Type:RNA  Length:22
                                                       
                1u6b C  191 AAGCCACACAAACCAGACGGCC    6
                                   200     ||  4  
                                         206|     
                                            1

Chain D from PDB  Type:RNA  Length:3
                                    
                1u6b D    3 CAu    1
                            |||
                            3||
                             2|
                              1-5MU

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, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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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	1u6b
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Description

Compounds