2OXC - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   HUMAN DEAD-BOX RNA HELICASE DDX20, DEAD DOMAIN IN COMPLEX WITH ADP

Authors :   T. Karlberg, D. Ogg, C. H Arrowsmith, H. Berglund, R. D. Busam, R. Collins, L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, B. M. Hallberg, M. Hammarstrom, M. Hogbom, I. Johansson, T. Kotenyova, L. Lehtio, M. Moche, P. Nordlund, T. Nyman, C. Persson, J. Sagemark, P. Stenmark, M. Sundstrom, A. G. Thorsell, S. Van Den Berg, J. Weigelt, L. Holmberg-Schiavone, Structural Genomics Consortium (Sgc)

Date :   20 Feb 07 (Deposition) - 27 Feb 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

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

Keywords :   Rna, Helicase, Dead, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Karlberg, D. Ogg, C. H Arrowsmith, H. Berglund, R. D. Busam, R. Collins, L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, B. M. Hallberg, M. Hammarstrom, M. Hogbom, I. Johansson, T. Kotenyova, L. Lehtio, M. Moche, P. Nordlund, T. Nyman, C. Persson, J. Sagemark, P. Stenmark, M. Sundstrom, A. G. Thorsell, S. Van Den Berg, J. Weigelt, L. Holmberg-Schiavone
Human Dead-Box Rna Helicase Ddx20
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROBABLE ATP-DEPENDENT RNA HELICASE DDX20
	Chains	:	A, B
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3)GOLD PRARE2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DEAD DOMAIN
	Gene	:	DDX20, DP103, GEMIN3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DEAD BOX PROTEIN 20, DEAD BOX PROTEIN DP 103, COMPONENT OF GEMS 3, GEMIN-3

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:82 , ARG A:84 , GLN A:89 , GLY A:109 , THR A:110 , GLY A:111 , LYS A:112 , THR A:113 , CYS A:114 , HOH A:355 , HOH A:441 , HOH A:501 , HOH A:524 , HOH A:602 , HOH A:605 , HOH A:608 , HOH A:613 , HOH A:647 , HOH A:655 , HOH A:658	BINDING SITE FOR RESIDUE ADP A 300
2	AC2	SOFTWARE	PHE B:82 , ARG B:84 , GLN B:89 , GLY B:109 , THR B:110 , GLY B:111 , LYS B:112 , THR B:113 , CYS B:114 , HOH B:304 , HOH B:315 , HOH B:355 , HOH B:457 , HOH B:543 , HOH B:546 , HOH B:573 , HOH B:582	BINDING SITE FOR RESIDUE ADP B 300

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	DDX20_HUMAN	62-90	2	A:62-90 B:62-90
2	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	DDX20_HUMAN	209-217	2	A:209-217 B:209-217

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	DDX20_HUMAN	62-90	1	A:62-90 -
2	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	DDX20_HUMAN	209-217	1	A:209-217 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	DDX20_HUMAN	62-90	1	- B:62-90
2	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	DDX20_HUMAN	209-217	1	- B:209-217

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000369702	1b	ENSE00001450683	chr1:112297927-112298847	921	DDX20_HUMAN	1-101	101	2	A:62-101 B:62-101	40 40
1.2	ENST00000369702	2	ENSE00000783731	chr1:112299268-112299362	95	DDX20_HUMAN	101-132	32	2	A:101-132 B:101-132	32 32
1.3	ENST00000369702	3	ENSE00000783732	chr1:112302022-112302190	169	DDX20_HUMAN	133-189	57	2	A:133-189 B:133-189	57 57
1.4b	ENST00000369702	4b	ENSE00000783733	chr1:112303096-112303210	115	DDX20_HUMAN	189-227	39	2	A:189-227 B:189-227	39 39
1.5a	ENST00000369702	5a	ENSE00000783734	chr1:112303328-112303470	143	DDX20_HUMAN	227-275	49	2	A:227-266 B:227-266	40 40
1.5c	ENST00000369702	5c	ENSE00000783735	chr1:112303609-112303747	139	DDX20_HUMAN	275-321	47	0	-	-
1.5e	ENST00000369702	5e	ENSE00000783736	chr1:112303848-112303906	59	DDX20_HUMAN	321-341	21	0	-	-
1.5f	ENST00000369702	5f	ENSE00000783737	chr1:112304877-112304959	83	DDX20_HUMAN	341-368	28	0	-	-
1.5i	ENST00000369702	5i	ENSE00000783741	chr1:112305299-112305404	106	DDX20_HUMAN	369-404	36	0	-	-
1.5j	ENST00000369702	5j	ENSE00000463721	chr1:112305528-112305629	102	DDX20_HUMAN	404-438	35	0	-	-
1.6c	ENST00000369702	6c	ENSE00001142728	chr1:112308359-112310638	2280	DDX20_HUMAN	438-824	387	0	-	-

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:205
 aligned with DDX20_HUMAN | Q9UHI6 from UniProtKB/Swiss-Prot  Length:824

    Alignment length:205
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     
          DDX20_HUMAN    62 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL 266
               SCOP domains d2oxca_ A: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains 2oxcA00 A:62-266 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh.......eeee....hhhhhhhhh....eeeehhhhhhhhhhh...hhhhh.eeee.hhhhhhh...hhhhhhhhhhhh....eeeeee...hhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE Q_MOTIF  PDB: A:62-90        ----------------------------------------------------------------------------------------------------------------------DEAD_ATP_------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:62-101 UniProt: 1-101 -------------------------------Exon 1.3  PDB: A:133-189 UniProt: 133-189                -------------------------------------Exon 1.5a  PDB: A:227-266 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.2  PDB: A:101-132        --------------------------------------------------------Exon 1.4b  PDB: A:189-227              --------------------------------------- Transcript 1 (2)
                 2oxc A  62 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL 266
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

Chain B from PDB  Type:PROTEIN  Length:205
 aligned with DDX20_HUMAN | Q9UHI6 from UniProtKB/Swiss-Prot  Length:824

    Alignment length:205
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261     
          DDX20_HUMAN    62 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL 266
               SCOP domains d2oxcb_ B: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains 2oxcB00 B:62-266 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         CATH domains
           Pfam domains (1) ------------------------DEAD-2oxcB01 B:86-253                                                                                                                                                   ------------- Pfam domains (1)
           Pfam domains (2) ------------------------DEAD-2oxcB02 B:86-253                                                                                                                                                   ------------- Pfam domains (2)
         Sec.struct. author ..hhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh.......eeee....hhhhhhhhh....eeeehhhhhhhhhhh...hhhhh.eeeeehhhhhhh...hhhhhhhhhhhh....eeeeee...hhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE Q_MOTIF  PDB: B:62-90        ----------------------------------------------------------------------------------------------------------------------DEAD_ATP_------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: B:62-101 UniProt: 1-101 -------------------------------Exon 1.3  PDB: B:133-189 UniProt: 133-189                -------------------------------------Exon 1.5a  PDB: B:227-266 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.2  PDB: B:101-132        --------------------------------------------------------Exon 1.4b  PDB: B:189-227              --------------------------------------- Transcript 1 (2)
                 2oxc B  62 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL 266
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

Legend:		→ Mismatch	(orange background)
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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 '\|'

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: automated matches (303)

Protein domain: automated matches (303)

Human (Homo sapiens) [TaxId: 9606] (86)

1a	d2oxca_	A:
1b	d2oxcb_	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	2oxcA00	A:62-266
1b	2oxcB00	B:62-266

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: DEAD (41)

Homo sapiens (Human) (12)

1a	DEAD-2oxcB01	B:86-253
1b	DEAD-2oxcB02	B:86-253

Asymmetric Unit(hide GO term definitions)

Chain A,B (DDX20_HUMAN | Q9UHI6)

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:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
	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.
	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:0030674	protein binding, bridging	The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0070491	repressing transcription factor binding	Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
biological process
	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:0010501	RNA secondary structure unwinding	The process in which a secondary structure of RNA are broken or 'melted'.
	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: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:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0051170	nuclear import	The directed movement of substances into the nucleus.
	GO:0048477	oogenesis	The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0050810	regulation of steroid biosynthetic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
	GO:0000387	spliceosomal snRNP assembly	The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome.
	GO:0000244	spliceosomal tri-snRNP complex assembly	The formation of a tri-snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. This includes reannealing of U4 and U6 (or U4atac and U6atac) snRNAs released from previous rounds of splicing to reform the U4/U6 snRNP (or U4atac/U6atac snRNP) as well as the subsequent association of the U5 snRNP with the U4/U6 snRNP (or U4atac/U6atac snRNP) to form a tri-snRNP that is ready to reassemble into another spliceosome complex.
cellular component
	GO:0097504	Gemini of coiled bodies	Nuclear bodies frequently found near or associated with Cajal bodies (also called coiled bodies or CBs). Gemini of coiled bodies, or 'gems', are similar in size and shape to CBs, and often indistinguishable under the microscope. Unlike CBs, gems do not contain small nuclear ribonucleoproteins (snRNPs); they contain a protein called survivor of motor neurons (SMN) whose function relates to snRNP biogenesis. Gems are believed to assist CBs in snRNP biogenesis, and to play a role in the etiology of spinal muscular atrophy (SMA).
	GO:0090571	RNA polymerase II transcription repressor complex	A protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription from a RNA polymerase II promoter.
	GO:0032797	SMN complex	A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus.
	GO:0034719	SMN-Sm protein complex	A protein complex formed by the association of several methylated Sm proteins with the SMN complex; the latter contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and unrip proteins; additional proteins, including galectin-1 and galectin-3, are also found in the SMN-SM complex. The SMN-Sm complex is involved in spliceosomal snRNP assembly in the cytoplasm.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.
	GO:0017053	transcriptional repressor complex	A protein complex that possesses activity that prevents or downregulates transcription.

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