2WAY - JenaLib

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Title :   STRUCTURE OF THE HUMAN DDX6 C-TERMINAL DOMAIN IN COMPLEX WITH AN EDC3-FDF PEPTIDE

Authors :   F. Tritschler, O. Weichenrieder

Date :   18 Feb 09 (Deposition) - 24 Mar 09 (Release) - 24 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Dead-Box Protein, Nucleotide-Binding, P54, Rck, Mirna, P-Bodies, Helicase, Decapping, Rna-Binding, Proto-Oncogene, Phosphoprotein, Chromosomal Rearrangement, Atp-Dependent Rna Helicase, Hydrolase, Cytoplasm, Mrna Decay, Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Tritschler, J. E. Braun, A. Eulalio, V. Truffault, E. Izaurralde, O. Weichenrieder
Structural Basis For The Mutually Exclusive Anchoring Of P Body Components Edc3 And Tral To The Dead Box Protein Ddx6/Me31B.
Mol. Cell V. 33 661 2009
PubMed-ID: 19285948 | Reference-DOI: 10.1016/J.MOLCEL.2009.02.014

Molecule 1 - ATP-DEPENDENT RNA HELICASE DDX6
	Chains	:	A, C
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSFDUET-1
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	562
	Fragment	:	C-TERMINAL DOMAIN, RESIDUES 296-483
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HUMAN DDX6, DEAD BOX PROTEIN 6, ATP-DEPENDENT RNA HELICASE P54, ONCOGENE RCK

Molecule 2 - ENHANCER OF MRNA-DECAPPING PROTEIN 3
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSFDUET-1
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	562
	Fragment	:	FDF PEPTIDE, RESIDUES 192-228
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HUMAN EDC3, LSM16 HOMOLOG, YJEF DOMAIN-CONTAINING PROTEIN 1, YJEF N-TERMINAL DOMAIN-CONTAINING PROTEIN 2, YJEF_N2, HYJEF_N2

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:334 , GLU A:337 , PHE C:318 , ILE C:323 , TYR C:348 , ARG C:375 , ASN C:376	BINDING SITE FOR RESIDUE GOL C1463
2	AC2	SOFTWARE	PHE A:351 , TYR A:352 , MET A:357 , HIS A:361 , VAL A:365	BINDING SITE FOR RESIDUE GOL A1461
3	AC3	SOFTWARE	GLU A:307 , LYS A:310 , ASN A:331 , ASP A:399 , LYS A:402 , ASP A:431 , HOH A:2037 , HOH A:2038	BINDING SITE FOR RESIDUE GOL A1462
4	AC4	SOFTWARE	PHE A:318 , TYR A:348 , ARG A:375 , ASN A:376 , GLN C:334 , GLU C:337	BINDING SITE FOR RESIDUE GOL A1463

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

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

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

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

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000315127	1	ENSE00001292931	chr15:74988384-74988221	164	EDC3_HUMAN	-	0	0	-	-
1.2b	ENST00000315127	2b	ENSE00001253727	chr15:74967483-74967302	182	EDC3_HUMAN	1-55	55	0	-	-
1.3	ENST00000315127	3	ENSE00001253676	chr15:74964115-74963796	320	EDC3_HUMAN	55-162	108	0	-	-
1.4	ENST00000315127	4	ENSE00001253669	chr15:74948409-74948074	336	EDC3_HUMAN	162-274	113	2	B:199-224 D:196-225	26 30
1.5	ENST00000315127	5	ENSE00001253663	chr15:74932960-74932807	154	EDC3_HUMAN	274-325	52	0	-	-
1.6	ENST00000315127	6	ENSE00001253655	chr15:74927967-74927750	218	EDC3_HUMAN	325-398	74	0	-	-
1.7b	ENST00000315127	7b	ENSE00001856853	chr15:74925287-74922899	2389	EDC3_HUMAN	398-508	111	0	-	-

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:153
 aligned with DDX6_HUMAN | P26196 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:165
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466     
           DDX6_HUMAN   307 KGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVA 471
               SCOP domains d2waya_ A: automated matches                                                                                                                                          SCOP domains
               CATH domains 2wayA00 A:296-460 P-loop containing nucleotide triphosphate hydrolases                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhh....eeee...-----....eeeeee.....hhhhhhhhhh-------.eeeeeeehhhhhhhhhhhhhhhh...ee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2way A 296 KGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDL-----DIQAVNVVINFDFPKLAETYLHRIG-------LGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVA 460
                                   305       315       325       335       345       355       365       375      |  -  |    395       405      |  -    |  425       435       445       455     
                                                                                                                382   388                     412     420

Chain B from PDB  Type:PROTEIN  Length:26
 aligned with EDC3_HUMAN | Q96F86 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:26
                                   208       218      
           EDC3_HUMAN   199 IPDTDFDFEGNLALFDKAAVFEEIDT 224
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
               Transcript 1 Exon 1.4  PDB: B:199-224   Transcript 1
                 2way B 199 IPDTDFDFEGNLALFDKAAVFEEIDT 224
                                   208       218

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with DDX6_HUMAN | P26196 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:166
                                   317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467      
           DDX6_HUMAN   308 GVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEY 473
               SCOP domains d2wayc_ C: automated matches                                                                                                                                           SCOP domains
               CATH domains 2wayC00 C:297-462 P-loop containing nucleotide triphosphate hydrolases                                                                                                 CATH domains
           Pfam domains (1) --------------------------------------------Helicase_C-2wayC01 C:341-412                                                   ------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------Helicase_C-2wayC02 C:341-412                                                   ------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh....ee.....hhhhhhhhhhhhhh....eeee...-------..eeeeee.....hhhhhhhhhh-------.eeeeeeehhhhhhhhhhhhhhhh...ee.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2way C 297 GVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDL-------QAVNVVINFDFPKLAETYLHRIG-------LGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEY 462
                                   306       316       326       336       346       356       366       376     |   -   |   396       406     |   -   |   426       436       446       456      
                                                                                                               382     390                   412     420

Chain D from PDB  Type:PROTEIN  Length:30
 aligned with EDC3_HUMAN | Q96F86 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:30
                                   205       215       225
           EDC3_HUMAN   196 IEEIPDTDFDFEGNLALFDKAAVFEEIDTY 225
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
           Pfam domains (1) --FDF-2wayD01 D:198-225        Pfam domains (1)
           Pfam domains (2) --FDF-2wayD02 D:198-225        Pfam domains (2)
         Sec.struct. author .........hhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
               Transcript 1 Exon 1.4  PDB: D:196-225       Transcript 1
                 2way D 196 IEEIPDTDFDFEGNLALFDKAAVFEEIDTY 225
                                   205       215       225

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: automated matches (303)

Protein domain: automated matches (303)

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

1a	d2waya_	A:
1b	d2wayc_	C:

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	2wayA00	A:296-460
1b	2wayC00	C:297-462

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Helicase_C (51)

Homo sapiens (Human) (15)

1a	Helicase_C-2wayC01	C:341-412
1b	Helicase_C-2wayC02	C:341-412

Clan: no clan defined [family: FDF] (2)

Family: FDF (2)

Homo sapiens (Human) (2)

2a	FDF-2wayD01	D:198-225
2b	FDF-2wayD02	D:198-225

Asymmetric Unit(hide GO term definitions)

Chain A,C (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.

Chain B,D (EDC3_HUMAN | Q96F86)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:1990174	phosphodiesterase decapping endonuclease activity	Catalysis of the removal of the cap from an unmethylated 5'-end capped RNA resulting in the release of the entire cap structure (GpppN) and a 5' monophosphorylated RNA.
	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).
biological process
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	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:0031087	deadenylation-independent decapping of nuclear-transcribed mRNA	Cleavage of the 5'-cap of a nuclear-transcribed mRNA that is independent of poly(A) tail shortening.
	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.
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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

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	DDX6_HUMAN \| P26196	:	1vec 2wax 4crw 4ct4 4ct5 5anr
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1vec	CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF RCK/P54, AHUMAN DEAD-BOX PROTEIN
2vc8	CRYSTAL STRUCTURE OF THE LSM DOMAIN OF HUMAN EDC3 (ENHANCER OF DECAPPING 3)
2wax	STRUCTURE OF THE HUMAN DDX6 C-TERMINAL DOMAIN IN COMPLEX WITH AN EDC3-FDF PEPTIDE

Description

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Ligands, Modified Residues, Ions (1, 4)

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