2E29 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE GUCT DOMAIN FROM HUMAN ATP-DEPENDENT RNA HELICASE DDX50, DEAD BOX PROTEIN 50

Authors :   S. Ohnishi, K. Paakkonen, P. Guntert, M. Sato, S. Koshiba, T. Harada, S. Watanabe, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   10 Nov 06 (Deposition) - 15 May 07 (Release) - 02 Dec 08 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Atp Binding, Helicase, Hydrolase, Nuclear Protein, Nucleotide-Binding, Rna-Binding, Guct Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ohnishi, K. Paakkonen, S. Koshiba, N. Tochio, M. Sato, N. Kobayashi, T. Harada, S. Watanabe, Y. Muto, P. Guntert, A. Tanaka, T. Kigawa, S. Yokoyama
Solution Structure Of The Guct Domain From Human Rna Helicase Ii/Gubeta Reveals The Rrm Fold, But Implausible Rna Interactions
Proteins V. 74 133 2008
PubMed-ID: 18615715 | Reference-DOI: 10.1002/PROT.22138
(for further references see the PDB file header)

Molecule 1 - ATP-DEPENDENT RNA HELICASE DDX50
	Chains	:	A
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	CELL-FREE PROTEIN SYNTHESIS
	Expression System Plasmid	:	P060403-01
	Expression System Vector Type	:	PLASMID
	Fragment	:	GUCT DOMAIN, RESIDUES 8-92
	Gene	:	DDX50
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DEAD BOX PROTEIN 50, NUCLEOLAR PROTEIN GU2, GU- BETA


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2E29)

(no "Site" information available for 2E29)

(no "SS Bond" information available for 2E29)

(no "Cis Peptide Bond" information available for 2E29)

(no "SAP(SNP)/Variant" information available for 2E29)

(no "PROSITE Motif" information available for 2E29)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000373585	1a	ENSE00001461052	chr10:70661034-70661227	194	DDX50_HUMAN	1-29	29	0	-	-
1.4	ENST00000373585	4	ENSE00000933680	chr10:70666467-70666763	297	DDX50_HUMAN	30-128	99	0	-	-
1.5	ENST00000373585	5	ENSE00000834206	chr10:70670063-70670138	76	DDX50_HUMAN	129-154	26	0	-	-
1.6b	ENST00000373585	6b	ENSE00001026806	chr10:70670824-70671002	179	DDX50_HUMAN	154-213	60	0	-	-
1.7b	ENST00000373585	7b	ENSE00000834207	chr10:70672918-70673035	118	DDX50_HUMAN	214-253	40	0	-	-
1.8b	ENST00000373585	8b	ENSE00000933681	chr10:70673147-70673332	186	DDX50_HUMAN	253-315	63	0	-	-
1.9	ENST00000373585	9	ENSE00000707030	chr10:70673815-70673960	146	DDX50_HUMAN	315-363	49	0	-	-
1.10a	ENST00000373585	10a	ENSE00000707041	chr10:70679588-70679737	150	DDX50_HUMAN	364-413	50	0	-	-
1.11	ENST00000373585	11	ENSE00000707057	chr10:70693955-70694116	162	DDX50_HUMAN	414-467	54	0	-	-
1.12b	ENST00000373585	12b	ENSE00001026805	chr10:70694555-70694674	120	DDX50_HUMAN	468-507	40	0	-	-
1.13b	ENST00000373585	13b	ENSE00001026811	chr10:70695762-70695835	74	DDX50_HUMAN	508-532	25	0	-	-
1.14	ENST00000373585	14	ENSE00001026819	chr10:70696692-70696851	160	DDX50_HUMAN	532-585	54	1	A:1-18 (gaps)	29
1.15	ENST00000373585	15	ENSE00001026801	chr10:70700816-70700950	135	DDX50_HUMAN	586-630	45	1	A:19-63	45
1.16	ENST00000373585	16	ENSE00001026810	chr10:70702969-70703013	45	DDX50_HUMAN	631-645	15	1	A:64-78	15
1.17b	ENST00000373585	17b	ENSE00001460966	chr10:70706108-70706603	496	DDX50_HUMAN	646-737	92	1	A:79-92	14

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:92
 aligned with DDX50_HUMAN | Q9BQ39 from UniProtKB/Swiss-Prot  Length:737

    Alignment length:103
                                   566       576       586       596       606       616       626       636       646       656   
          DDX50_HUMAN   557 GAVDALAAALAHISGASSFEPRSLITSDKGFVTMTLESLEEIQDVSCAWKELNRKLSSNAVSQITRMCLLKGNMGVCFDVPTTESERLQAEWHDSDWILSVPA 659
               SCOP domains ------------------d2e29a1 A:8-92 ATP-dependent RNA helicase DDX50                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------.................eeeeeee.......hhhhhhhhhhhhhhhhhh..eeeee.....eeeeeeehhhhhhhhhhh.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.14  PDB: A:1-18 (gaps)Exon 1.15  PDB: A:19-63 UniProt: 586-630     Exon 1.16      Exon 1.17b     Transcript 1
                 2e29 A   1 GS-----------SGSSGFEPRSLITSDKGFVTMTLESLEEIQDVSCAWKELNRKLSSNAVSQITRMCLLKGNMGVCFDVPTTESERLQAEWHDSDWILSVPA  92
                             |       -   |     9        19        29        39        49        59        69        79        89   
                             2           3

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(

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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: GUCT domain (1)

Protein domain: ATP-dependent RNA helicase DDX50 (1)

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

d2e29a1

A:8-92

(no "CATH Domain" information available for 2E29)

(no "Pfam Domain" information available for 2E29)

NMR Structure(hide GO term definitions)

Chain A (DDX50_HUMAN | Q9BQ39)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004004	ATP-dependent RNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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:0010501	RNA secondary structure unwinding	The process in which a secondary structure of RNA are broken or 'melted'.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

NMR Structure
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	2e29
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