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Description

Title :   SOLUTION STRUCTURE OF THE RPR DOMAIN OF PUTATIVE RNA-BINDING PROTEIN 16

Authors :   W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   30 Mar 06 (Deposition) - 30 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Nmr, Structure Genomics, Rpr Domain, Putative Rna-Binding Protein 16, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of The Rpr Domain Of Putative Rna-Binding Protein 16
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - PUTATIVE RNA-BINDING PROTEIN 16
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P050719-03
	Expression System Vector Type	:	PLASMID
	Fragment	:	RPR DOMAIN
	Gene	:	RBM16; KIAA1116
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE PROTEIN SYNTHESIS
	Synonym	:	RNA BINDING MOTIF PROTEIN 16, KIAA1116 PROTEIN

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

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

Sites (0, 0)

(no "Site" information available for 2DIW)

SS Bonds (0, 0)

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

Cis Peptide Bonds (1, 20)

NMR Structure

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20	Pro A:28	-	Pro A:29

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2DIW)

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CID	PS51391	CID domain profile.	SCAF8_HUMAN	1-139	1	A:10-146

Exons (6, 6)

NMR Structure (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000367178	1a	ENSE00001428900	chr6:155054459-155055064	606	SCAF8_HUMAN	1-10	10	1	A:10-19	10
1.3	ENST00000367178	3	ENSE00002165709	chr6:155095123-155095206	84	SCAF8_HUMAN	11-38	28	1	A:20-47	28
1.4	ENST00000367178	4	ENSE00002190306	chr6:155099135-155099179	45	SCAF8_HUMAN	39-53	15	1	A:48-62	15
1.5	ENST00000367178	5	ENSE00002183742	chr6:155108995-155109156	162	SCAF8_HUMAN	54-107	54	1	A:63-116	54
1.6c	ENST00000367178	6c	ENSE00001237781	chr6:155113957-155114110	154	SCAF8_HUMAN	108-159	52	1	A:117-152 (gaps)	52
1.7	ENST00000367178	7	ENSE00000813828	chr6:155116143-155116273	131	SCAF8_HUMAN	159-202	44	1	A:152-152	1
1.8	ENST00000367178	8	ENSE00001237766	chr6:155123105-155123281	177	SCAF8_HUMAN	203-261	59	0	-	-
1.9	ENST00000367178	9	ENSE00000813830	chr6:155124678-155124757	80	SCAF8_HUMAN	262-288	27	0	-	-
1.10	ENST00000367178	10	ENSE00000813831	chr6:155126503-155126620	118	SCAF8_HUMAN	288-327	40	0	-	-
1.11	ENST00000367178	11	ENSE00001237750	chr6:155129204-155129335	132	SCAF8_HUMAN	328-371	44	0	-	-
1.12	ENST00000367178	12	ENSE00000813833	chr6:155129820-155129932	113	SCAF8_HUMAN	372-409	38	0	-	-
1.13	ENST00000367178	13	ENSE00001237733	chr6:155131149-155131342	194	SCAF8_HUMAN	409-474	66	0	-	-
1.14	ENST00000367178	14	ENSE00001375840	chr6:155136850-155136950	101	SCAF8_HUMAN	474-507	34	0	-	-
1.15	ENST00000367178	15	ENSE00001190014	chr6:155139613-155139726	114	SCAF8_HUMAN	508-545	38	0	-	-
1.16	ENST00000367178	16	ENSE00001237706	chr6:155141311-155141467	157	SCAF8_HUMAN	546-598	53	0	-	-
1.17b	ENST00000367178	17b	ENSE00001237697	chr6:155143410-155143543	134	SCAF8_HUMAN	598-642	45	0	-	-
1.18	ENST00000367178	18	ENSE00000813840	chr6:155145368-155145512	145	SCAF8_HUMAN	643-691	49	0	-	-
1.20	ENST00000367178	20	ENSE00001237676	chr6:155148306-155148374	69	SCAF8_HUMAN	691-714	24	0	-	-
1.21	ENST00000367178	21	ENSE00000813842	chr6:155152056-155152274	219	SCAF8_HUMAN	714-787	74	0	-	-
1.22b	ENST00000367178	22b	ENSE00001812832	chr6:155153073-155155192	2120	SCAF8_HUMAN	787-1271	485	0	-	-

Sequences/Alignments

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
	(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:152
 aligned with SCAF8_HUMAN | Q9UPN6 from UniProtKB/Swiss-Prot  Length:1271

    Alignment length:168
                                     1                                                                                                                                                              
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
          SCAF8_HUMAN     - ---------MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAGIPPPVVTPVLASTTTAMSNTPG 159
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.........hhhhhhhhhhhhhh....hhhhhhhhhh......----------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------CID  PDB: A:10-146 UniProt: 1-139                                                                                                          -------------------- PROSITE
           Transcript 1 (1) ---------Exon 1.1a Exon 1.3  PDB: A:20-47      Exon 1.4       Exon 1.5  PDB: A:63-116 UniProt: 54-107               Exon 1.6c  PDB: A:117-152 (gaps) UniProt: 108-159    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------1 Transcript 1 (2)
                 2diw A   1 GSSGSSGDNMEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAGSGP----------------SSG 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        |-         -     |  
                                                                                                                                                                              149              150

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)

(no "SCOP Domain" information available for 2DIW)

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2DIW)

Gene Ontology (11, 11)

NMR Structure(hide GO term definitions)

Chain A (SCAF8_HUMAN | Q9UPN6)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0043175	RNA polymerase core enzyme binding	Interacting selectively and non-covalently with an RNA polymerase core enzyme, containing a specific subunit composition defined as the core enzyme.
	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).
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.
cellular component
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	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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	SCAF8_HUMAN \| Q9UPN6	:	3d9i 3d9j 3d9k 3d9l 3d9m 3d9n 3d9o 3d9p

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