4BRU - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE YEAST DHH1-EDC3 COMPLEX

Authors :   H. Sharif, S. Ozgur, K. Sharma, C. Basquin, H. Urlaub, E. Conti

Date :   05 Jun 13 (Deposition) - 24 Jul 13 (Release) - 09 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.24

Chains :   Asym./Biol. Unit : A,B

Keywords :   Hydrolase, Decapping, Translational Repression, Mrnp Remodel P-Body, Dead-Box (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Sharif, S. Ozgur, K. Sharma, C. Basquin, H. Urlaub, E. Conti
Structural Analysis Of The Yeast Dhh1-Pat1 Complex Reveals How Dhh1 Engages Pat1, Edc3 And Rna In Mutually Exclusive Interactions
Nucleic Acids Res. V. 41 8377 2013
PubMed-ID: 23851565 | Reference-DOI: 10.1093/NAR/GKT600

Molecule 1 - ATP-DEPENDENT RNA HELICASE DHH1
	Atcc	:	204508
	Chains	:	A
	EC Number	:	3.6.4.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	GOLD PLYSS
	Fragment	:	RESIDUES 46-422
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	S288C
	Synonym	:	DEXD/H-BOX HELICASE 1

Molecule 2 - ENHANCER OF MRNA-DECAPPING PROTEIN 3
	Atcc	:	204508
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	GOLD PLYSS
	Fragment	:	RESIDUES 77-116
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	S288C

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4BRU)

(no "Site" information available for 4BRU)

(no "SS Bond" information available for 4BRU)

(no "Cis Peptide Bond" information available for 4BRU)

(no "SAP(SNP)/Variant" information available for 4BRU)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	DHH1_YEAST	46-74	1	A:46-74
2	DFDF	PS51512	DFDF domain profile.	EDC3_YEAST	93-129	1	B:93-116
3	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	DHH1_YEAST	193-201	1	A:193-201

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDL160C	1	YDL160C.1	IV:171931-170411	1521	DHH1_YEAST	1-506	506	1	A:46-420	375

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:375
 aligned with DHH1_YEAST | P39517 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:375
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415     
           DHH1_YEAST    46 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEELTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDKSLYVA 420
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhhhhhhhh....hhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh......eeee....hhhhhhhhh.....eeeehhhhhhhhhhh.........eeee.hhhhhhhhhhhhhhhhhhh......eeeeee.......hhhhhhhh...eeee.........eeeeeee....hhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...eeee..............eeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhh...eee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE Q_MOTIF  PDB: A:46-74        ----------------------------------------------------------------------------------------------------------------------DEAD_ATP_--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:46-420 UniProt: 1-506 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 4bru A  46 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVDEFMDKHLHKPYEINLMEELTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDKSLYVA 420
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415

Chain B from PDB  Type:PROTEIN  Length:29
 aligned with EDC3_YEAST | P39998 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:29
                                    97       107         
           EDC3_YEAST    88 HIDWQDDDVSKIKQQEDFDFQRNLGMFNK 116
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE -----DFDF  PDB: B:93-116      PROSITE
                 Transcript ----------------------------- Transcript
                 4bru B  88 HIDWQDDDVSKIKQQEDFDFQRNLGMFNK 116
                                    97       107

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 '\|'

(no "SCOP Domain" information available for 4BRU)

(no "CATH Domain" information available for 4BRU)

(no "Pfam Domain" information available for 4BRU)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DHH1_YEAST | P39517)

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:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	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: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: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:0090079	translation regulator activity, nucleic acid binding	Any selective and non-covalent interaction with a nucleic acid involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
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:0000290	deadenylation-dependent decapping of nuclear-transcribed mRNA	Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.
	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: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:0017148	negative regulation of translation	Any process that stops, prevents, or reduces 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:0045900	negative regulation of translational elongation	Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation.
	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:0034063	stress granule assembly	The aggregation, arrangement and bonding together of proteins and RNA molecules to form a stress granule.
	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: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:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.

Chain B (EDC3_YEAST | P39998)

molecular function
	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: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: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:1900153	positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.
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: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.

Asymmetric/Biological Unit
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	DHH1_YEAST \| P39517
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	EDC3_YEAST \| P39998
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UniProtKB/Swiss-Prot
	DHH1_YEAST \| P39517	:	1s2m 4brw

4brw	CRYSTAL STRUCTURE OF THE YEAST DHH1-PAT1 COMPLEX

Description

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