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Description

Title :   SOLUTION STRUCTURE OF DSRM DOMAIN IN SPERMATID PERINUCLEAR RNA-BIND PROTEIN

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

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

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Nmr, Dsrm Domain, 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. Kadirvel, F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Dsrm Domain In Spermatid Perinuclear Rna-Bind Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - SPERMATID PERINUCLEAR RNA-BINDING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P051128-11
	Expression System Vector Type	:	PLASMID
	Fragment	:	DSRM DOMAIN
	Gene	:	STRBP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE PROTEIN SYNTHESIS

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 2DMY)

Sites (0, 0)

(no "Site" information available for 2DMY)

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	STRBP_HUMAN	387-453 510-576	1	A:17-83 -

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000348403	1c	ENSE00001461091	chr9:126030843-126030715	129	STRBP_HUMAN	-	0	0	-	-
1.2	ENST00000348403	2	ENSE00001327887	chr9:125999245-125999109	137	STRBP_HUMAN	-	0	0	-	-
1.6b	ENST00000348403	6b	ENSE00002156923	chr9:125946577-125946411	167	STRBP_HUMAN	1-1	1	0	-	-
1.8	ENST00000348403	8	ENSE00002182268	chr9:125941506-125941286	221	STRBP_HUMAN	2-75	74	0	-	-
1.9a	ENST00000348403	9a	ENSE00001287138	chr9:125936121-125935956	166	STRBP_HUMAN	75-130	56	0	-	-
1.10	ENST00000348403	10	ENSE00001769379	chr9:125932325-125932181	145	STRBP_HUMAN	131-179	49	0	-	-
1.12	ENST00000348403	12	ENSE00001751996	chr9:125923347-125923256	92	STRBP_HUMAN	179-209	31	0	-	-
1.13	ENST00000348403	13	ENSE00001763512	chr9:125922741-125922646	96	STRBP_HUMAN	210-241	32	0	-	-
1.14	ENST00000348403	14	ENSE00001784370	chr9:125921486-125921375	112	STRBP_HUMAN	242-279	38	0	-	-
1.15	ENST00000348403	15	ENSE00001630656	chr9:125920708-125920611	98	STRBP_HUMAN	279-311	33	0	-	-
1.16	ENST00000348403	16	ENSE00001595442	chr9:125920402-125920291	112	STRBP_HUMAN	312-349	38	1	A:1-2	2
1.17	ENST00000348403	17	ENSE00001748247	chr9:125910149-125910057	93	STRBP_HUMAN	349-380	32	1	A:2-10 (gaps)	32
1.18	ENST00000348403	18	ENSE00001739862	chr9:125909333-125909134	200	STRBP_HUMAN	380-446	67	1	A:10-76	67
1.19	ENST00000348403	19	ENSE00001768279	chr9:125901966-125901808	159	STRBP_HUMAN	447-499	53	1	A:77-97	21
1.20a	ENST00000348403	20a	ENSE00001687364	chr9:125898794-125898660	135	STRBP_HUMAN	500-544	45	0	-	-
1.21a	ENST00000348403	21a	ENSE00001722654	chr9:125898460-125898320	141	STRBP_HUMAN	545-591	47	0	-	-
1.22a	ENST00000348403	22a	ENSE00001735311	chr9:125895247-125895124	124	STRBP_HUMAN	592-633	42	0	-	-
1.23	ENST00000348403	23	ENSE00001795039	chr9:125890537-125890493	45	STRBP_HUMAN	633-648	16	0	-	-
1.24d	ENST00000348403	24d	ENSE00001728022	chr9:125887952-125886990	963	STRBP_HUMAN	648-672	25	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:97
 aligned with STRBP_HUMAN | Q96SI9 from UniProtKB/Swiss-Prot  Length:672

    Alignment length:120
                                   357       367       377       387       397       407       417       427       437       447       457       467
          STRBP_HUMAN   348 EGAGSSALKRPFEDGLGDDKDPNKKMKRNLRKILDSKAIDLMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDADIECMSSD 467
               SCOP domains ------------------------------d2dmya1 A:8-91 Spermatid perinuclear RNA-binding protein                            ------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......--------.---------------............hhhhhhhhh......eeeeee......eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------DS_RBD  PDB: A:17-83 UniProt: 387-453                              -------------- PROSITE
           Transcript 1 (1) 1.------------------------------Exon 1.18  PDB: A:10-76 UniProt: 380-446                           Exon 1.19             Transcript 1 (1)
           Transcript 1 (2) -Exon 1.17  PDB: A:2-10 (gaps)   --------------------------------------------------------------------------------------- Transcript 1 (2)
                 2dmy A   1 GSSGSS--------G---------------RKILDSKAIDLMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGFDADISGPSSG  97
                                 |   -    |    -         -|       17        27        37        47        57        67        77        87        97
                                 6        7               8

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 (1, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: dsRBD-like (111)

Superfamily: dsRNA-binding domain-like (98)

Family: Double-stranded RNA-binding domain (dsRBD) (34)

Protein domain: Spermatid perinuclear RNA-binding protein (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2dmya1

A:8-91

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

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

Gene Ontology (13, 13)

NMR Structure(hide GO term definitions)

Chain A (STRBP_HUMAN | Q96SI9)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	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:0003727	single-stranded RNA binding	Interacting selectively and non-covalently with single-stranded RNA.
biological process
	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:0007638	mechanosensory behavior	Behavior that is dependent upon the sensation of a mechanical stimulus.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0007286	spermatid development	The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0015630	microtubule cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
	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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