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Title :   SOLUTION STRUCTURE OF DROSOPHILA MELANOGASTER SNF RBD1

Authors :   C. Liu, G. Cui, J. Hu, C. Jin, B. Xia

Date :   12 May 08 (Deposition) - 03 Jun 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Rna Binding Protein, Snf Rbd1, Rna Binding, Rna Splicing, Solution Structure, Mrna Processing, Mrna Splicing, Nucleus, Ribonucleoprotein, Rna-Binding, Spliceosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Hu, G. Cui, C. Li, C. Liu, C. Jin, J. Wang, B. Xia
Structural And Functional Studies Of Rna Splicing Factor Sans-Fille By Multidimentional Nmr Spectroscopy
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21D(+)
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Vector Type	:	PLASMID
	Fragment	:	RRM1 DOMAIN (UNP RESIDUES 1-98)
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Synonym	:	U1 SNRNP PROTEIN A, U1-A, SEX DETERMINATION PROTEIN SNF


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2K3K)

(no "Site" information available for 2K3K)

(no "SS Bond" information available for 2K3K)

(no "Cis Peptide Bond" information available for 2K3K)

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SNRPA_DROME_001 *	R	49	H	SNRPA_DROME	---	---	A	R	49	H
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	SNRPA_DROME	7-86 142-216	1	A:7-86 -

(no "Exon" information available for 2K3K)

NMR Structure

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:104
 aligned with SNRPA_DROME | P43332 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
          SNRPA_DROME     1 MEMLPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKERPKK 104
               SCOP domains d2k3ka1 A:1-104 Splicesomal U1A protein                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------RRM_1-2k3kA01 A:9-80                                                    ------------------------ Pfam domains
         Sec.struct. author .......eeee.......hhhhhhhhhhhhhhhhh.eeeee...hhhhh..eeeee.hhhhhhhhhhhhh..........eee...hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------H------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------RRM  PDB: A:7-86 UniProt: 7-86                                                  ------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2k3k A   1 MEMLPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKERPKK 104
                                    10        20        30        40        50        60        70        80        90       100

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: Canonical RBD (214)

Protein domain: Splicesomal U1A protein (46)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (3)

d2k3ka1

A:1-104

(no "CATH Domain" information available for 2K3K)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RRM (206)

Family: RRM_1 (131)

Drosophila melanogaster (Fruit fly) (8)

RRM_1-2k3kA01

A:9-80

NMR Structure(hide GO term definitions)

Chain A (SNRPA_DROME | P43332)

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:0030620	U2 snRNA binding	Interacting selectively and non-covalently with the U2 small nuclear RNA (U2 snRNA).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	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:0008266	poly(U) RNA binding	Interacting selectively and non-covalently with a sequence of uracil residues in an RNA molecule.
	GO:0097158	pre-mRNA intronic pyrimidine-rich binding	Interacting selectively and non-covalently with a pyrimidine-rich (CU-rich) intronic sequence of a pre-messenger RNA (pre-mRNA).
	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:0019099	female germ-line sex determination	The determination of sex and sexual phenotype in a female organism's germ line.
	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.
	GO:0048477	oogenesis	The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
	GO:0007539	primary sex determination, soma	The transmission of information about sexual status from the initial, general, determination to signals specific to the soma.
	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
cellular component
	GO:0005685	U1 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U1.
	GO:0005686	U2 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U2.
	GO:0071013	catalytic step 2 spliceosome	A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	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:0071011	precatalytic spliceosome	A spliceosomal complex that is formed by the recruitment of a preassembled U5-containing tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the associated snRNPs.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0030532	small nuclear ribonucleoprotein complex	A complex composed of RNA of the small nuclear RNA (snRNA) class and protein, found in the nucleus of a eukaryotic cell. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP or U4/U6 snRNP. Many, but not all, of these complexes are involved in splicing of nuclear mRNAs.
	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.

NMR Structure
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