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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE N-TERMINAL RNA BINDING DOMAIN IN DAZ-ASSOCIATED PROTEIN 1

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

Date :   23 Mar 06 (Deposition) - 23 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

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

Molecule 1 - DAZ-ASSOCIATED PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P050704-07
	Expression System Vector Type	:	PLASMID
	Fragment	:	RNA RECOGNITION MOTIF
	Gene	:	DAZAP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	DELETED IN AZOOSPERMIA-ASSOCIATED PROTEIN 1


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2DH8)

(no "Site" information available for 2DH8)

(no "SS Bond" information available for 2DH8)

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	Arg A:71	-	Pro A:72

(no "SAP(SNP)/Variant" information available for 2DH8)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	DAZP1_HUMAN	10-97 113-190	1	A:10-92 -

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000233078	1	ENSE00001180932	chr19:1407584-1407801	218	DAZP1_HUMAN	1-10	10	1	A:1-10	10
1.2	ENST00000233078	2	ENSE00001266753	chr19:1417499-1417539	41	DAZP1_HUMAN	10-24	15	1	A:10-24	15
1.3	ENST00000233078	3	ENSE00001266707	chr19:1418203-1418369	167	DAZP1_HUMAN	24-79	56	1	A:24-79	56
1.4	ENST00000233078	4	ENSE00001266698	chr19:1418665-1418730	66	DAZP1_HUMAN	80-101	22	1	A:80-93	14
1.5	ENST00000233078	5	ENSE00000336445	chr19:1421147-1421257	111	DAZP1_HUMAN	102-138	37	1	A:94-98	5
1.6	ENST00000233078	6	ENSE00000336446	chr19:1422347-1422395	49	DAZP1_HUMAN	139-155	17	0	-	-
1.7	ENST00000233078	7	ENSE00000752956	chr19:1425877-1425959	83	DAZP1_HUMAN	155-182	28	0	-	-
1.8	ENST00000233078	8	ENSE00000752955	chr19:1428841-1428994	154	DAZP1_HUMAN	183-234	52	0	-	-
1.9	ENST00000233078	9	ENSE00000752954	chr19:1429966-1429995	30	DAZP1_HUMAN	234-244	11	0	-	-
1.10	ENST00000233078	10	ENSE00000752953	chr19:1430221-1430361	141	DAZP1_HUMAN	244-291	48	0	-	-
1.11	ENST00000233078	11	ENSE00000752952	chr19:1432513-1432689	177	DAZP1_HUMAN	291-350	60	0	-	-
1.13	ENST00000233078	13	ENSE00001605245	chr19:1434736-1435683	948	DAZP1_HUMAN	350-407	58	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:105
 aligned with DAZP1_HUMAN | Q96EP5 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:115
                                   1                                                                                                           
                                   | 3        13        23        33        43        53        63        73        83        93       103     
          DAZP1_HUMAN     - -------MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPERTRPKEGWQKGPRSD 108
               SCOP domains d2dh8a_ A: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................ee.........hhhhhhhhhhh...eeeeeeee......eeeeeeeee...hhhhhhhhhh.eee..eee.............----------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------RRM  PDB: A:10-92 UniProt: 10-97                                                        ----------- PROSITE
           Transcript 1 (1) -------Exon 1.1  -------------Exon 1.3  PDB: A:24-79 UniProt: 24-79                   Exon 1.4  PDB: A:80-931.5     Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.2       ------------------------------------------------------------------------------------ Transcript 1 (2)
                 2dh8 A  -6 GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPS----------GPSSG  98
                                     3        13        23        33        43        53        63        73        83        93         -|    
                                                                                                                              93         94

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 '\|'

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: automated matches (67)

Protein domain: automated matches (67)

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

d2dh8a_

(no "CATH Domain" information available for 2DH8)

(no "Pfam Domain" information available for 2DH8)

NMR Structure(hide GO term definitions)

Chain A (DAZP1_HUMAN | Q96EP5)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0035613	RNA stem-loop binding	Interacting selectively and non-covalently with a stem-loop in an RNA molecule. An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop.
	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.
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:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0001893	maternal placenta development	Maternally driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
	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:0048026	positive regulation of mRNA splicing, via spliceosome	Any process that activates or increases the rate or extent of mRNA splicing via a spliceosomal mechanism.
	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: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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(no "Sites" information available for 2dh8)

	Cis Peptide Bonds
		Arg A:71 - Pro A:72	[ RasMol ]

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	2dh8
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Description

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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (1, 20)

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Exons (5, 5)

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