Structure of PDB 5okz Chain a

Receptor sequence

>5okza (length=227) Species: 559292 (Saccharomyces cerevisiae S288C)

MSTFIFPGDSFPVDPTTPVKLGPGIYCDPNTQEIRPVNTGVLHVQTAYID
YSSKRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKK
NRPTLQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDV
NLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEELSNTLACY
RTIMECCQKNDTAAFKDIAKRQFKEIL

3D structure

• PDB: 5okz Mpp6 Incorporation in the Nuclear Exosome Contributes to RNA Channeling through the Mtr4 Helicase.
• Chain: a
• Resolution: 3.20004 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	peptide	a	Y120 G146 L150 L167 F168 F184 E185 V186	Y112 G138 L142 L159 F160 F176 E177 V178

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0030145 manganese ion binding

Biological Process

• GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
• 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:0000956 nuclear-transcribed mRNA catabolic process
• GO:0006364 rRNA processing
• GO:0006396 RNA processing
• GO:0006401 RNA catabolic process
• GO:0034475 U4 snRNA 3'-end processing
• GO:0071034 CUT catabolic process
• GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process
• GO:0071038 TRAMP-dependent tRNA surveillance pathway
• GO:0071051 poly(A)-dependent snoRNA 3'-end processing

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

External links

• PDB: RCSB:5okz, PDBe:5okz, PDBj:5okz
• PDBsum: 5okz
• PubMed: 28877463
• UniProt: Q08285|RRP40_YEAST Exosome complex component RRP40 (Gene Name=RRP40)