3PEV - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   S. CEREVISIAE DBP5 L327V C-TERMINAL DOMAIN BOUND TO GLE1 AND IP6

Authors :   B. Montpetit, N. D. Thomsen, K. J. Helmke, M. A. Seeliger, J. M. Berger, K

Date :   27 Oct 10 (Deposition) - 23 Mar 11 (Release) - 27 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Reca, Heat, Dead-Box, Atpase, Helicase, Mrna Export, Nuclear Pore, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Montpetit, N. D. Thomsen, K. J. Helmke, M. A. Seeliger, J. M. Berger, K. Weis
A Conserved Mechanism Of Dead-Box Atpase Activation By Nucleoporins And Insp(6) In Mrna Export.
Nature V. 472 238 2011
PubMed-ID: 21441902 | Reference-DOI: 10.1038/NATURE09862

Molecule 1 - ATP-DEPENDENT RNA HELICASE DBP5
	Chains	:	A
	EC Number	:	3.6.4.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3) RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DBP5-CTD
	Gene	:	DBP5, RAT8, YOR046C
	Mutation	:	YES
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	DEAD BOX PROTEIN 5, HELICASE CA5/6, RIBONUCLEIC ACID- TRAFFICKING PROTEIN 8

Molecule 2 - NUCLEOPORIN GLE1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3) RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BRR3, D1049, GLE1, RSS1, YDL207W
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	NUCLEAR PORE PROTEIN GLE1, RNA EXPORT FACTOR GLE1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	IHP	1	Ligand/Ion	INOSITOL HEXAKISPHOSPHATE
3	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 16)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	IHP	1	Ligand/Ion	INOSITOL HEXAKISPHOSPHATE
3	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	IHP	1	Ligand/Ion	INOSITOL HEXAKISPHOSPHATE
3	MSE	7	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:339 , LYS A:340 , HOH A:1008 , LYS B:510	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	VAL A:389 , ASP A:406 , LEU A:407 , THR A:409 , ARG A:423 , HOH A:1018 , LEU B:462 , ASN B:463	BINDING SITE FOR RESIDUE GOL A 1002
3	AC3	SOFTWARE	LYS A:477 , LYS A:481 , LYS B:264 , LYS B:333 , HIS B:337 , ARG B:374 , LYS B:377 , LYS B:378 , HOH B:1037 , HOH B:1047 , HOH B:1048 , HOH B:1076	BINDING SITE FOR RESIDUE IHP B 1003
4	AC4	SOFTWARE	ILE B:389 , ASN B:411 , ASP B:415 , THR B:466 , ASN B:467 , HOH B:1052	BINDING SITE FOR RESIDUE GOL B 1004
5	AC5	SOFTWARE	PHE B:246 , ILE B:249 , GLY B:384 , THR B:386 , ARG B:456 , PRO B:461	BINDING SITE FOR RESIDUE GOL B 1005

(no "SS Bond" information available for 3PEV)

(no "Cis Peptide Bond" information available for 3PEV)

(no "SAP(SNP)/Variant" information available for 3PEV)

(no "PROSITE Motif" information available for 3PEV)

(no "Exon" information available for 3PEV)

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:178
 aligned with DBP5_YEAST | P20449 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:180
                                   312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482
           DBP5_YEAST   303 AIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWDEVEKIVKKVLKD 482
               SCOP domains d3peva_ A: automated matches                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------------Helicase_C-3pevA01 A:348-431                                                        --------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeee............eeeeee...........hhhhhhhhhhhhh--....eeeeee.hhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pev A 303 AIKQLYmDCKNEADKFDVLTELYGVmTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSmVVNYDLPTLANGQADPATYIHRIGRTG--GRKGVAISFVHDKNSFNILSAIQKYFGDIEmTRVPTDDWDEVEKIVKKVLKD 482
                                  |312       322     | 332       342       352       362       372       382       392       402       412       422     | 432       442       452       462       472       482
                                  |                328-MSE                                                                  401-MSE                    428  |                           461-MSE                 
                                309-MSE                                                                                                                   431

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with GLE1_YEAST | Q12315 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:295
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533     
           GLE1_YEAST   244 TNFDKISKMFWHYKDKIAQIKQDIVLPIKKADVNVRNLLSRHKRKINPKFGQLTNSNQQLFKIQNELTQLINDTKGDSLAYHWILNFIAKAVVHQAETEVRVKPESALPLGKLTLYLLVQFPELQELFMARLVKKCPFVIGFTCEIDTEKGRQNMGWKRNNENKWEDNTSYDERMGGILSLFAIITRLQLPQEFITTTSHPFPIALSWHILARICNTPLNLITNTHFVILGSWWDAAAVQFLQAYGNQASKLLILIGEELTSRMAEKKYVGAARLRILLEAWQNNNMESFPEMSP 538
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------GLE1-3pevB01 B:256-502                                                                                                                                                                                                                                 ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pev B 244 TNFDKISKmFWHYKDKIAQIKQDIVLPIKKADVNVRNLLSRHKRKINPKFGQLTNSNQQLFKIQNELTQLINDTKGDSLAYHWILNFIAKAVVHQAETEVRVKPESALPLGKLTLYLLVQFPELQELFmARLVKKCPFVIGFTCEIDTEKGRQNmGWKRNNENKWEDNTSYDERmGGILSLFAIITRLQLPQEFITTTSHPFPIALSWHILARICNTPLNLITNTHFVILGSWWDAAAVQFLQAYGNQASKLLILIGEELTSRmAEKKYVGAARLRILLEAWQNNNmESFPEmSP 538
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393    |  403       413    |  423       433       443       453       463       473       483       493       503   |   513       523      |533  |  
                                  252-MSE                                                                                                                 372-MSE                   398-MSE             418-MSE                                                                                  507-MSE                530-MSE |  
                                                                                                                                                                                                                                                                                                                              536-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (8)

d3peva_

(no "CATH Domain" information available for 3PEV)

Asymmetric Unit(hide GO term definitions)

Chain A (DBP5_YEAST | P20449)

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:0008186	RNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
	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:0000822	inositol hexakisphosphate binding	Interacting selectively and non-covalently with inositol hexakisphosphate.
	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).
biological process
	GO:0010501	RNA secondary structure unwinding	The process in which a secondary structure of RNA are broken or 'melted'.
	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:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006415	translational termination	The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
	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:0005934	cellular bud tip	The end of a cellular bud distal to the site of attachment to the mother cell.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	GO:0044614	nuclear pore cytoplasmic filaments	Filamentous extensions on cytoplasmic face of the nuclear pore complex (NPC). In S. cerevisiae, Nup159p, Nup82p, and Nup42p contribute to the cytoplasmic filaments. In vertebrates, Nup358 is a major component.
	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:0005844	polysome	A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.

Chain B (GLE1_YEAST | Q12315)

molecular function
	GO:0008047	enzyme activator activity	Binds to and increases the activity of an enzyme.
	GO:0000822	inositol hexakisphosphate binding	Interacting selectively and non-covalently with inositol hexakisphosphate.
	GO:0005543	phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
	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:0031369	translation initiation factor binding	Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation.
biological process
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	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:0016973	poly(A)+ mRNA export from nucleus	The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006446	regulation of translational initiation	Any process that modulates the frequency, rate or extent of translational initiation.
	GO:0006449	regulation of translational termination	Any process that modulates the frequency, rate or extent of translational termination.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	GO:0044614	nuclear pore cytoplasmic filaments	Filamentous extensions on cytoplasmic face of the nuclear pore complex (NPC). In S. cerevisiae, Nup159p, Nup82p, and Nup42p contribute to the cytoplasmic filaments. In vertebrates, Nup358 is a major component.
	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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	DBP5_YEAST \| P20449	:	2kbe 2kbf 3gfp 3peu 3pew 3pey 3rrm 3rrn 5elx
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