Structure of PDB 4ifd Chain J Binding Site BS01

Receptor Information
>4ifd Chain J (length=948) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RRKRLADGLSVTQKVFVRSRNGGATKIVREHYLRSDIPCLSRSCTKCPQI
VVPDAQNELPKFILSDSPLELSAPIGKHYVVLDTNVVLQAIDLLENPNCF
FDVIVPQIVLDEVRNKSYPVYTRLRTLCRDSDDHKRFIVFHNEFSEHTFV
ERLPNETINDRNNRAIRKTCQWYSEHLKPYDINVVLVTNDRLNREAATKE
VESNIITKSLVQYIELLPNADDIRDSIPQTFSDFTFPEYYSTARVMGGLK
NGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQVIVE
LLPQSEWKAPVISDKQRRLLAKDAMIAQRSKKIQPTAKVVYIQRRSWRQY
VGQLAPSSVDPQSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISI
DSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPFSKKVLECL
PAEGHDWKAPTKLDDPEAVSKDPLLTKRKDLRDKLICSIDPPGCVDINDA
LHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDM
LPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFS
YEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKV
HMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLR
RHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNT
LVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVV
AHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQFAGRASIEYYV
GQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAF
DEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK
Ligand information
>4ifd Chain R (length=30) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ccccgagaggggguuuuuuuuuuuuuuuuu
<<<<....>>>>..................
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4ifd Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.
Resolution2.805 Å
Binding residue
(original residue number in PDB)		N277 Q315 D543 P544 C547 D549 I550 N551 D552 Y595 Y654 L696 V727 E728 M731 L732 R753 H755 T810 M813 A815 A816 H831 Y839 H841 T843 R847 R882 R889 R896
Binding residue
(residue number reindexed from 1)		N258 Q296 D490 P491 C494 D496 I497 N498 D499 Y542 Y601 L643 V674 E675 M678 L679 R700 H702 T757 M760 A762 A763 H778 Y786 H788 T790 R794 R829 R836 R843
Enzymatic activity
Catalytic site (original residue number in PDB) D543 D549 N551 D552 Y654 R847
Catalytic site (residue number reindexed from 1) D490 D496 N498 D499 Y601 R794
Enzyme Commision number 3.1.13.-
3.1.26.-
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000175 3'-5'-RNA exonuclease activity
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004519 endonuclease activity
GO:0004521 RNA endonuclease activity
GO:0004527 exonuclease activity
GO:0004540 RNA nuclease activity
GO:0005515 protein binding
Biological Process
GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0006397 mRNA processing
GO:0006401 RNA catabolic process
GO:0016075 rRNA catabolic process
GO:0043628 regulatory ncRNA 3'-end processing
GO:0070651 nonfunctional rRNA decay
GO:0071028 nuclear mRNA surveillance
GO:0071031 nuclear mRNA surveillance of mRNA 3'-end processing
GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process
GO:0071038 TRAMP-dependent tRNA surveillance pathway
GO:0071039 nuclear polyadenylation-dependent CUT catabolic process
Cellular Component
GO:0000176 nuclear exosome (RNase complex)
GO:0000177 cytoplasmic exosome (RNase complex)
GO:0000178 exosome (RNase complex)
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005739 mitochondrion

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4ifd, PDBe:4ifd, PDBj:4ifd
PDBsum4ifd
PubMed23376952
UniProtQ08162|RRP44_YEAST Exosome complex exonuclease DIS3 (Gene Name=DIS3)

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