2RB4 - JenaLib

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Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HELICASE DOMAIN OF HUMAN DDX25 RNA HELICASE

Authors :   L. Lehtio, M. Hogbom, J. Uppenberg, C. H. Arrowsmith, H. Berglund, A. M. M. Ehn, S. Flodin, A. Flores, S. Graslund, B. M. Hallberg, M. Hammarstr T. Kotenyova, P. Nilsson-Ehle, P. Nordlund, T. Nyman, D. Ogg, C. Perss J. Sagemark, P. Stenmark, M. Sundstrom, A. G. Thorsell, S. Van Den Be J. Weigelt, L. Holmberg-Schiavone, Structural Genomics Consorti

Date :   18 Sep 07 (Deposition) - 02 Oct 07 (Release) - 27 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Rna Helicase, Rossmann Fold, Structural Genomics, Structural Genomics Consortium, Sgc, Alternative Initiation, Atp-Binding, Developmental Protein, Differentiation, Hydrolase, Mrna Transport, Nucleotide- Binding, Nucleus, Phosphorylation, Rna-Binding, Spermatogenesis, Translation Regulation, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Schutz, T. Karlberg, S. Van Den Berg, R. Collins, L. Lehtio, M. Hogbom, L. Holmberg-Schiavone, W. Tempel, H. W. Park, M. Hammarstrom, M. Moche, A. G. Thorsell, H. Schuler
Comparative Structural Analysis Of Human Dead-Box Rna Helicases.
Plos One V. 5 12791 2010
PubMed-ID: 20941364 | Reference-DOI: 10.1371/JOURNAL.PONE.0012791

Molecule 1 - ATP-DEPENDENT RNA HELICASE DDX25
	Chains	:	A, B
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	HELICASE DOMAIN: RESIDUES 307-479
	Gene	:	DDX25, GRTH
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DEAD BOX PROTEIN 25, GONADOTROPIN-REGULATED TESTICULAR RNA HELICASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SO4	1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:400	BINDING SITE FOR RESIDUE CL A 1
2	AC2	SOFTWARE	ARG A:348	BINDING SITE FOR RESIDUE CL A 2
3	AC3	SOFTWARE	LEU A:307 , GLN B:382 , ARG B:385	BINDING SITE FOR RESIDUE SO4 B 1
4	AC4	SOFTWARE	GLN A:382 , ARG A:385	BINDING SITE FOR RESIDUE SO4 A 480
5	AC5	SOFTWARE	CYS A:398 , HIS A:430 , CYS B:398 , ARG B:400 , HIS B:430	BINDING SITE FOR RESIDUE ZN A 481

(no "SS Bond" information available for 2RB4)

(no "Cis Peptide Bond" information available for 2RB4)

(no "SAP(SNP)/Variant" information available for 2RB4)

(no "PROSITE Motif" information available for 2RB4)

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000263576	2a	ENSE00000994957	chr11:125774258-125774475	218	DDX25_HUMAN	1-21	21	0	-	-
1.4a	ENST00000263576	4a	ENSE00000994958	chr11:125775107-125775173	67	DDX25_HUMAN	22-44	23	0	-	-
1.5	ENST00000263576	5	ENSE00000994956	chr11:125775448-125775492	45	DDX25_HUMAN	44-59	16	0	-	-
1.6b	ENST00000263576	6b	ENSE00000994955	chr11:125775969-125776104	136	DDX25_HUMAN	59-104	46	0	-	-
1.7	ENST00000263576	7	ENSE00001132664	chr11:125778091-125778183	93	DDX25_HUMAN	104-135	32	0	-	-
1.8	ENST00000263576	8	ENSE00001160018	chr11:125778296-125778398	103	DDX25_HUMAN	135-169	35	0	-	-
1.9b	ENST00000263576	9b	ENSE00001093879	chr11:125780259-125780373	115	DDX25_HUMAN	170-208	39	0	-	-
1.10a	ENST00000263576	10a	ENSE00001093823	chr11:125781206-125781383	178	DDX25_HUMAN	208-267	60	0	-	-
1.11	ENST00000263576	11	ENSE00000749522	chr11:125786909-125787146	238	DDX25_HUMAN	267-346	80	2	A:307-346 B:307-346	40 40
1.12	ENST00000263576	12	ENSE00000749510	chr11:125788523-125788685	163	DDX25_HUMAN	347-401	55	2	A:347-401 B:347-401	55 55
1.13b	ENST00000263576	13b	ENSE00000749508	chr11:125791086-125791274	189	DDX25_HUMAN	401-464	64	2	A:401-464 (gaps) B:401-464 (gaps)	64 64
1.14c	ENST00000263576	14c	ENSE00002176428	chr11:125792715-125793005	291	DDX25_HUMAN	464-483	20	2	A:464-476 B:464-476	13 13

Asymmetric Unit

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:164
 aligned with DDX25_HUMAN | Q9UHL0 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:170
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476
          DDX25_HUMAN   307 LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAEDMD 476
               SCOP domains d2rb4a_ A: ATP-dependent RNA helicase DDX25                                                                                                                                SCOP domains
               CATH domains 2rb4A00 A:307-476 P-loop containing nucleotide triphosphate hydrolases                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..hhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh....eeee............eeeeee.....--....hhhhhhhhhh..----..eeeeeeehhhhhhhhhhhhhhhh...eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: A:307-346 [INCOMPLETE]  Exon 1.12  PDB: A:347-401 UniProt: 347-401             --------------------------------------------------------------Exon 1.14c    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.13b  PDB: A:401-464 (gaps) UniProt: 401-464              ------------ Transcript 1 (2)
                 2rb4 A 307 LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPV--GEEPDYETYLHRIGRT----KKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAEDMD 476
                                   316       326       336       346       356       366       376       386       396       406       416|  |   426        |-   |   446       456       466       476
                                                                                                                                        417  |            435  440                                    
                                                                                                                                           420

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with DDX25_HUMAN | Q9UHL0 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:170
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476
          DDX25_HUMAN   307 LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAEDMD 476
               SCOP domains d2rb4b_ B: ATP-dependent RNA helicase DDX25                                                                                                                                SCOP domains
               CATH domains 2rb4B00 B:307-476 P-loop containing nucleotide triphosphate hydrolases                                                                                                     CATH domains
           Pfam domains (1) -------------------------------------------------Helicase_C-2rb4B01 B:356-435                                                         ------------------------------------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------------Helicase_C-2rb4B02 B:356-435                                                         ------------------------------------ Pfam domains (2)
         Sec.struct. author .....eeeeeee..hhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh....eeee............eeeeee.....--....hhhhhhhhhh..-----.eeeeeeehhhhhhhhhhhhhhhh..eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: B:307-346 [INCOMPLETE]  Exon 1.12  PDB: B:347-401 UniProt: 347-401             --------------------------------------------------------------Exon 1.14c    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.13b  PDB: B:401-464 (gaps) UniProt: 401-464              ------------ Transcript 1 (2)
                 2rb4 B 307 LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPV--GEEPDYETYLHRIGRT-----KGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAEDMD 476
                                   316       326       336       346       356       366       376       386       396       406       416|  |   426        |-    |  446       456       466       476
                                                                                                                                        417  |            435   441                                   
                                                                                                                                           420

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Tandem AAA-ATPase domain (59)

Protein domain: ATP-dependent RNA helicase DDX25 (1)

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

1a	d2rb4a_	A:
1b	d2rb4b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Human (Homo sapiens) (413)

1a	2rb4A00	A:307-476
1b	2rb4B00	B:307-476

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Helicase_C (51)

Homo sapiens (Human) (15)

1a	Helicase_C-2rb4B01	B:356-435
1b	Helicase_C-2rb4B02	B:356-435

Asymmetric Unit(hide GO term definitions)

Chain A,B (DDX25_HUMAN | Q9UHL0)

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'.
	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:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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: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.
	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.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0033391	chromatoid body	A ribonucleoprotein complex found in the cytoplasm of male germ cells, composed of exceedingly thin filaments that are consolidated into a compact mass or into dense strands of varying thickness that branch to form an irregular network. Contains mRNAs, miRNAs, and protein components involved in miRNA processing (such as Argonaute proteins and the endonuclease Dicer) and in RNA decay (such as the decapping enzyme DCP1a and GW182).
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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Description

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Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

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