Structure of PDB 5c0w Chain J Binding Site BS01

Receptor Information
>5c0w Chain J (length=970) 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
VESNIITKSLVQYIELLPNADDIRDSIPQMTFSDFTFPEYYSTARVMGGL
KNGVLYQGNIQISEYNFLEGSVSLPRFSKPVLIVGQKNLNRAFNGDQVIV
ELLPQSEWKAPSSIVLDSEHFDVNDNPDINTTVISDKQRRLLAKDAMIAQ
RSKKIQPTAKVVYIQRRSWRQYVGQLAPSSVDPQSSSTQNVFVILMDKCL
PKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAET
EALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTKR
KDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGT
ALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELD
DSANIVNVNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLS
VKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFM
LLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLE
SSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRH
YGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMIC
RNINRKHRNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVP
KFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEV
QVRSVMDPITSKRKAELLLK
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5c0w RNA degradation paths in a 12-subunit nuclear exosome complex.
Resolution4.6 Å
Binding residue
(original residue number in PDB)		N277 R397 D543 P544 C547 D549 N551 Y595 Y654 L696 E728 M731 L732 R753 H755 M813 M814 A815 A816 H831 L834 Y839 T843 R847 R889 R896
Binding residue
(residue number reindexed from 1)		N259 R366 D512 P513 C516 D518 N520 Y564 Y623 L665 E697 M700 L701 R722 H724 M782 M783 A784 A785 H800 L803 Y808 T812 R816 R858 R865
Enzymatic activity
Catalytic site (original residue number in PDB) D543 D549 N551 D552 Y654 R847
Catalytic site (residue number reindexed from 1) D512 D518 N520 D521 Y623 R816
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:5c0w, PDBe:5c0w, PDBj:5c0w
PDBsum5c0w
PubMed26222026
UniProtQ08162|RRP44_YEAST Exosome complex exonuclease DIS3 (Gene Name=DIS3)

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