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Description

Title :   SOLUTION STRUCTURE OF THE SECOND RNA BINDING DOMAIN OF RNA BINDING MOTIF PROTEIN 23

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

Date :   27 Apr 06 (Deposition) - 17 Apr 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Rna Recognition Motif, Rrm, Rna Binding Domain, Rbd, Rnp, 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 :   S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - PROBABLE RNA-BINDING PROTEIN 23
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P050516-02
	Expression System Vector Type	:	PLASMID
	Fragment	:	RNA RECOGNITION MOTIF
	Gene	:	RBM23
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	RNA-BINDING MOTIF PROTEIN 23, RNA- BINDING REGION- CONTAINING PROTEIN 4, SPLICING FACTOR SF2

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 2DNZ)

Sites (0, 0)

(no "Site" information available for 2DNZ)

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM23_HUMAN	263-341 166-243	1	A:231-307 -

Exons (3, 3)

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000359890	1	ENSE00001423747	chr14:23388396-23388208	189	RBM23_HUMAN	-	0	0	-	-
1.2	ENST00000359890	2	ENSE00002198998	chr14:23380612-23380537	76	RBM23_HUMAN	1-22	22	0	-	-
1.3	ENST00000359890	3	ENSE00001759900	chr14:23378804-23378692	113	RBM23_HUMAN	23-60	38	0	-	-
1.4	ENST00000359890	4	ENSE00001688900	chr14:23377589-23377542	48	RBM23_HUMAN	60-76	17	0	-	-
1.5b	ENST00000359890	5b	ENSE00001149981	chr14:23375577-23375404	174	RBM23_HUMAN	76-134	59	0	-	-
1.6	ENST00000359890	6	ENSE00001149977	chr14:23374868-23374815	54	RBM23_HUMAN	134-152	19	0	-	-
1.7	ENST00000359890	7	ENSE00000653785	chr14:23374662-23374545	118	RBM23_HUMAN	152-191	40	0	-	-
1.8	ENST00000359890	8	ENSE00001149963	chr14:23374455-23374303	153	RBM23_HUMAN	192-242	51	0	-	-
1.9	ENST00000359890	9	ENSE00001099497	chr14:23374221-23374084	138	RBM23_HUMAN	243-288	46	1	A:224-254	31
1.10	ENST00000359890	10	ENSE00001099492	chr14:23373535-23373470	66	RBM23_HUMAN	289-310	22	1	A:255-276	22
1.12	ENST00000359890	12	ENSE00001099495	chr14:23371591-23371396	196	RBM23_HUMAN	311-376	66	1	A:277-318 (gaps)	55
1.13	ENST00000359890	13	ENSE00001099490	chr14:23371308-23371189	120	RBM23_HUMAN	376-416	41	0	-	-
1.14	ENST00000359890	14	ENSE00001432222	chr14:23371092-23371023	70	RBM23_HUMAN	416-439	24	0	-	-
1.15	ENST00000359890	15	ENSE00001413847	chr14:23370942-23369855	1088	RBM23_HUMAN	439-439	1	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
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Chain A from PDB  Type:PROTEIN  Length:95
 aligned with RBM23_HUMAN | Q86U06 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:108
                                   267       277       287       297       307       317       327       337       347       357        
          RBM23_HUMAN   258 GNGGPMRLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDGGTDITFPDGDQELDLGSAGG 365
               SCOP domains d2dnza_ A: RNA binding protein 23                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeee.......hhhhhhhh.....eeeeee...........eeeeee..hhhhhhhhhhh..........eeee.........-------------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----RRM  PDB: A:231-307 UniProt: 263-341                                           ------------------------ PROSITE
               Transcript 1 Exon 1.9  PDB: A:224-254       Exon 1.10             Exon 1.12  PDB: A:277-318 (gaps) UniProt: 311-376       Transcript 1
                 2dnz A 224 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDGGS-------------GPSSG 318
                                   233       243       253       263       273       283       293       303       313         -   |    
                                                                                                                   313           314

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: Canonical RBD (214)

Protein domain: RNA binding protein 23 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d2dnza_

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

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

Gene Ontology (7, 7)

NMR Structure(hide GO term definitions)

Chain A (RBM23_HUMAN | Q86U06)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

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Related Entries

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	RBM23_HUMAN \| Q86U06	:	2cq4

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