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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH DOMAIN-CONTAINING PROTEIN 1 (PUTATIVE SPLICING FACTOR YT521)

Authors :   F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Tarada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   06 Apr 07 (Deposition) - 09 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Nmr, Structure Genomics, Yth Domain, Yth Domain-Containing Protein 1 (Putative Splicing Factor Yt521), 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 :   F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Tarada, S. Yokoyama
Solution Structure Of The Yth Domain In Yth Domain-Containing Protein 1 (Putative Splicing Factor Yt521)
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - YTH DOMAIN-CONTAINING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P060508-15
	Expression System Vector Type	:	PLASMID
	Fragment	:	YTH DOMAIN
	Gene	:	YTHDC1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	PUTATIVE SPLICING FACTOR YT521


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2YUD)

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

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

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	YTH	PS50882	YTH domain profile.	YTDC1_HUMAN	355-492	1	A:26-163

NMR Structure (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000344157	1a	ENSE00001406123	chr4:69215807-69215444	364	YTDC1_HUMAN	1-10	10	0	-	-
1.3b	ENST00000344157	3b	ENSE00001139471	chr4:69204102-69204001	102	YTDC1_HUMAN	10-44	35	0	-	-
1.4c	ENST00000344157	4c	ENSE00001331970	chr4:69203618-69203290	329	YTDC1_HUMAN	44-153	110	0	-	-
1.5	ENST00000344157	5	ENSE00000969898	chr4:69203168-69202745	424	YTDC1_HUMAN	154-295	142	0	-	-
1.6	ENST00000344157	6	ENSE00001072477	chr4:69199115-69199026	90	YTDC1_HUMAN	295-325	31	1	A:1-4	4
1.7	ENST00000344157	7	ENSE00001220825	chr4:69198565-69198512	54	YTDC1_HUMAN	325-343	19	1	A:5-14	10
1.8	ENST00000344157	8	ENSE00001072483	chr4:69197915-69197821	95	YTDC1_HUMAN	343-374	32	1	A:14-45	32
1.9	ENST00000344157	9	ENSE00001072479	chr4:69196028-69195920	109	YTDC1_HUMAN	375-411	37	1	A:46-82	37
1.10a	ENST00000344157	10a	ENSE00001072476	chr4:69195837-69195720	118	YTDC1_HUMAN	411-450	40	1	A:82-121	40
1.11	ENST00000344157	11	ENSE00001012578	chr4:69189941-69189857	85	YTDC1_HUMAN	450-478	29	1	A:121-149	29
1.12a	ENST00000344157	12a	ENSE00001012580	chr4:69188633-69188467	167	YTDC1_HUMAN	479-534	56	1	A:150-180	31
1.13	ENST00000344157	13	ENSE00001072482	chr4:69185923-69185841	83	YTDC1_HUMAN	534-562	29	0	-	-
1.14	ENST00000344157	14	ENSE00001012548	chr4:69184580-69184544	37	YTDC1_HUMAN	562-574	13	0	-	-
1.15a	ENST00000344157	15a	ENSE00001072474	chr4:69184447-69184408	40	YTDC1_HUMAN	574-587	14	0	-	-
1.16	ENST00000344157	16	ENSE00001072480	chr4:69184299-69184237	63	YTDC1_HUMAN	588-608	21	0	-	-
1.17a	ENST00000344157	17a	ENSE00001012568	chr4:69182166-69182032	135	YTDC1_HUMAN	609-653	45	0	-	-
1.18b	ENST00000344157	18b	ENSE00001524098	chr4:69180041-69176105	3937	YTDC1_HUMAN	654-727	74	0	-	-

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

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Chain A from PDB  Type:PROTEIN  Length:180
 aligned with YTDC1_HUMAN | Q96MU7 from UniProtKB/Swiss-Prot  Length:727

    Alignment length:194
                                   325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505    
          YTDC1_HUMAN   316 GSSASESYAGSEKKHEKLSSSVRAVRKDQTSKLKYVLQDARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARSVILIFSVRESGKFQGFARLSSESHHGGSPIHWVLPAGMSAKMLGGVFKIDWICRRELPFTKSAHLTNPWNEHKPVKIGRDGQEIELECGTQLCLLFPPDESIDLYQVIHKMRH 509
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------YTH-2yudA01 A:25-166                                                                                                                          -------------- Pfam domains
         Sec.struct. author ....--------------...........hhhhhhh....eeeeeee..hhhhhhhhhh.ee...hhhhhhhhhhhhh...eeeeeee....eeeeeeeeeeeee...............hhhh..eeeeeeee...eehhhh...ee.....ee.......eee.hhhhhhhhhh.........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------YTH  PDB: A:26-163 UniProt: 355-492                                                                                                       ----------------- PROSITE
           Transcript 1 (1) Exon 1.6  -----------------Exon 1.8  PDB: A:14-45          ------------------------------------Exon 1.10a  PDB: A:82-121               ----------------------------Exon 1.12a  PDB: A:150-180      Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.7           -------------------------------Exon 1.9  PDB: A:46-82               --------------------------------------Exon 1.11  PDB: A:121-149    ------------------------------- Transcript 1 (2)
                 2yud A   1 GSSG--------------SSGVRAVRKDQTSKLKYVLQDARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARSVILIFSVRESGKFQGFARLSSESHHGGSPIHWVLPAGMSAKMLGGVFKIDWICRRELPFTKSAHLTNPWNEHKPVKIGRDGQEIELECGTQLCLLFPPDESIDLYQVIHKMRH 180
                               |     -        |6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176    
                               4              5

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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

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

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PUA (42)

Family: YTH (2)

Homo sapiens (Human) (2)

YTH-2yudA01

A:25-166

NMR Structure(hide GO term definitions)

Chain A (YTDC1_HUMAN | Q96MU7)

molecular function
	GO:1990247	N6-methyladenosine-containing RNA binding	Interacting selectively and non-covalently with an RNA molecule modified by N6-methyladenosine (m6A), a modification present at internal sites of mRNAs and some non-coding RNAs.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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.
	GO:0006376	mRNA splice site selection	Selection of a splice site by components of the assembling spliceosome.
	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:0048024	regulation of mRNA splicing, via spliceosome	Any process that modulates the frequency, rate or extent of mRNA splicing via a spliceosomal mechanism.
cellular component
	GO:0016604	nuclear body	Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	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.

NMR Structure
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