1VEC - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF RCK/P54, A HUMAN DEAD-BOX PROTEIN

Authors :   K. Hogetsu, T. Matsui, Y. Yukihiro, M. Tanaka, T. Sato, T. Kumasaka, N. Tanaka

Date :   29 Mar 04 (Deposition) - 13 Apr 04 (Release) - 29 Apr 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Rna Helicase, Dead-Box Protein, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Matsui, K. Hogetsu, J. Usukura, T. Sato, T. Kumasaka, Y. Akao, N. Tanaka
Structural Insight Of Human Dead-Box Protein Rck/P54 Into Its Substrate Recognition With Conformational Changes
Genes Cells V. 11 439 2006
PubMed-ID: 16611246 | Reference-DOI: 10.1111/J.1365-2443.2006.00951.X
(for further references see the PDB file header)

Molecule 1 - ATP-DEPENDENT RNA HELICASE P54
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTYB11
	Expression System Strain	:	ER2566
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN
	Gene	:	HUMRCK
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RCK, DEAD-BOX PROTEIN 6

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID
2	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	TLA	-1	Ligand/Ion	L(+)-TARTARIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	TLA	-1	Ligand/Ion	L(+)-TARTARIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:102 , HIS A:179 , GLU B:106 , ASP B:202	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	ARG A:128 , THR A:268 , PHE A:269 , PRO A:270 , HOH A:1070 , HOH A:1108 , ARG B:163 , THR B:189 , GLY B:190 , THR B:211 , GLY B:213 , ARG B:214 , HOH B:2002 , HOH B:2014 , HOH B:2017	BINDING SITE FOR RESIDUE TLA B 2001

(no "SS Bond" information available for 1VEC)

(no "Cis Peptide Bond" information available for 1VEC)

(no "SAP(SNP)/Variant" information available for 1VEC)

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.	DDX6_HUMAN	96-124	2	A:85-113 B:85-113
2	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	DDX6_HUMAN	244-252	2	A:233-241 B:233-241

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.	DDX6_HUMAN	96-124	1	A:85-113 -
2	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	DDX6_HUMAN	244-252	1	A:233-241 -

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.	DDX6_HUMAN	96-124	1	- B:85-113
2	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	DDX6_HUMAN	244-252	1	- B:233-241

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	DDX6_HUMAN	96-124	2	A:85-113 B:85-113
2	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	DDX6_HUMAN	244-252	2	A:233-241 B:233-241

(no "Exon" information available for 1VEC)

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:206
 aligned with DDX6_HUMAN | P26196 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:206
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293      
           DDX6_HUMAN    94 KGNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEIN 299
               SCOP domains d1veca_ A: DEAD box RNA helicase rck/p54                                                                                                                                                                       SCOP domains
               CATH domains 1vecA00 A:83-288 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..hhhhhhhhhh......hhhhhhhhhhhhh...eeee......hhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh.......eeee....hhhhhhhhh.....eeeehhhhhhhhhhh.........eeeeehhhhhh...hhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --Q_MOTIF  PDB: A:85-113       -----------------------------------------------------------------------------------------------------------------------DEAD_ATP_----------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vec A  83 KGNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEIN 288
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

Chain B from PDB  Type:PROTEIN  Length:206
 aligned with DDX6_HUMAN | P26196 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:206
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293      
           DDX6_HUMAN    94 KGNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEIN 299
               SCOP domains d1vecb_ B: DEAD box RNA helicase rck/p54                                                                                                                                                                       SCOP domains
               CATH domains 1vecB00 B:83-288 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                          CATH domains
           Pfam domains (1) --------------------------DEAD-1vecB01 B:109-276                                                                                                                                                  ------------ Pfam domains (1)
           Pfam domains (2) --------------------------DEAD-1vecB02 B:109-276                                                                                                                                                  ------------ Pfam domains (2)
         Sec.struct. author ...hhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhh....eeeehhhhhhhhhhh.........eeeeehhhhhh...hhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --Q_MOTIF  PDB: B:85-113       -----------------------------------------------------------------------------------------------------------------------DEAD_ATP_----------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vec B  83 KGNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEIN 288
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

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: DEAD box RNA helicase rck/p54 (1)

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

1a	d1veca_	A:
1b	d1vecb_	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	1vecA00	A:83-288
1b	1vecB00	B:83-288

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: DEAD (41)

Homo sapiens (Human) (12)

1a	DEAD-1vecB01	B:109-276
1b	DEAD-1vecB02	B:109-276

Asymmetric Unit(hide GO term definitions)

Chain A,B (DDX6_HUMAN | P26196)

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:0003724	RNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
	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.
	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:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
biological process
	GO:0010501	RNA secondary structure unwinding	The process in which a secondary structure of RNA are broken or 'melted'.
	GO:0033962	cytoplasmic mRNA processing body assembly	The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
	GO:0043928	exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 3'-poly(A) tail.
	GO:0045665	negative regulation of neuron differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
	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:0019827	stem cell population maintenance	The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
	GO:0019074	viral RNA genome packaging	The packaging of viral RNA (single-stranded or double-stranded) into a nucleocapsid.
cellular component
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0016442	RISC complex	A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	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:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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