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Title :   SOLUTION STRUCTURE OF RNA BINDING DOMAIN 1 IN RNA-BINDING PROTEIN 30

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

Date :   26 Apr 06 (Deposition) - 26 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Rrm Domain, Rbd, 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 :   K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - RNA-BINDING PROTEIN 4B
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P050704-15
	Expression System Vector Type	:	PLASMID
	Fragment	:	RNA RECOGNITION MOTIF
	Gene	:	RBM30
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	RNA-BINDING MOTIF PROTEIN 4B, RNA-BINDING PROTEIN 30, RNA-BINDING MOTIF PROTEIN 30


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2DNQ)

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

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

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

NMR Structure (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM4B_HUMAN	2-72 78-148	2	A:2-72 A:83-83
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM4_HUMAN	2-72 78-148	2	A:2-72 A:83-83

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000310092	1a	ENSE00002199787	chr11:66406088-66406223	136	RBM4_HUMAN	-	0	0	-	-
1.2b	ENST00000310092	2b	ENSE00002159170	chr11:66407171-66407594	424	RBM4_HUMAN	1-138	138	1	A:1-83	83
1.3b	ENST00000310092	3b	ENSE00002140504	chr11:66410921-66411611	691	RBM4_HUMAN	138-364	227	0	-	-
1.5e	ENST00000310092	5e	ENSE00002150086	chr11:66413498-66413940	443	RBM4_HUMAN	-	0	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

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:90
 aligned with RBM4B_HUMAN | Q9BQ04 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:90
                                   1                                                                                  
                                   | 3        13        23        33        43        53        63        73        83
           RBM4B_HUMAN    - -------MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASTKLHVG 83
               SCOP domains d2dnqa_ A: automated matches                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee......hhhhhhhhhhh...eeeeeee..eeeeee.hhhhhhhhhhhhh.........eee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------RRM  PDB: A:2-72 UniProt: 2-72                                         -----RRM    PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  2dnq A -6 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASSGPSSG 83
                                     3        13        23        33        43        53        63        73        83

Chain A from PDB  Type:PROTEIN  Length:90
 aligned with RBM4_HUMAN | Q9BWF3 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:90
                                   1                                                                                  
                                   | 3        13        23        33        43        53        63        73        83
            RBM4_HUMAN    - -------MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKTSTKLHVG 83
               SCOP domains d2dnqa_ A: automated matches                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee......hhhhhhhhhhh...eeeeeee..eeeeee.hhhhhhhhhhhhh.........eee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------RRM  PDB: A:2-72 UniProt: 2-72                                         -----RRM    PROSITE
               Transcript 1 -------Exon 1.2b  PDB: A:1-83 UniProt: 1-138 [INCOMPLETE]                                  Transcript 1
                  2dnq A -6 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASSGPSSG 83
                                     3        13        23        33        43        53        63        73        83

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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( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: automated matches (67)

Protein domain: automated matches (67)

Human (Homo sapiens) [TaxId: 9606] (56)

d2dnqa_

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

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

NMR Structure(hide GO term definitions)

Chain A (RBM4B_HUMAN | Q9BQ04)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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:0032922	circadian regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
	GO:0007623	circadian rhythm	Any biological process in an organism that recurs with a regularity of approximately 24 hours.
	GO:0043153	entrainment of circadian clock by photoperiod	The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).
	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:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
cellular component
	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: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.

Chain A (RBM4_HUMAN | Q9BWF3)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003730	mRNA 3'-UTR binding	Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0035198	miRNA binding	Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes.
	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:0097157	pre-mRNA intronic binding	Interacting selectively and non-covalently with an intronic sequence of a pre-messenger RNA (pre-mRNA).
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0002192	IRES-dependent translational initiation of linear mRNA	The process where translation initiation recruits the 40S ribosomal subunits via an internal ribosome entry segment (IRES) before an AUG codon is encountered in an appropriate sequence context to initiate linear mRNA translation.
	GO:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	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:0002190	cap-independent translational initiation	The process where translation initiation recruits the 40S ribosomal subunits in a Cap and 5' end independent fashion before an AUG codon is encountered in an appropriate sequence context to initiate mRNA or circRNA translation.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0097167	circadian regulation of translation	Any process that modulates the frequency, rate or extent of mRNA translation with a regularity of approximately 24 hours.
	GO:0043153	entrainment of circadian clock by photoperiod	The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	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:0035278	miRNA mediated inhibition of translation	The process in which microRNAs (miRNAs) block the translation of target mRNAs into proteins. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA will typically mediate repression of translation if the miRNA imperfectly base-pairs with the 3' untranslated regions of target mRNAs
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0032055	negative regulation of translation in response to stress	Any process that stops, prevents or reduces the rate of translation as a result of a stimulus indicating the organism is under stress.
	GO:0045947	negative regulation of translational initiation	Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.
	GO:0051149	positive regulation of muscle cell differentiation	Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
	GO:0046822	regulation of nucleocytoplasmic transport	Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm.
	GO:0046685	response to arsenic-containing substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
	GO:0051403	stress-activated MAPK cascade	A series of molecular signals in which a stress-activated MAP kinase cascade relays one or more of the signals; MAP kinase cascades involve at least three protein kinase activities and culminate in the phosphorylation and activation of a MAP kinase.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	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: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.

NMR Structure
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