Structure of PDB 4ifd Chain B

Receptor sequence

>4ifdB (length=242) Species: 559292 (Saccharomyces cerevisiae S288C)

MSRLEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKII
TLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERSKSSHKNERRVLEI
QTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDA
GISMFDYISGISVGLYDTTPLLDTNSLEENAMSTVTLGVVGKSEKLSLLL
VEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQKRVSN

3D structure

• PDB: 4ifd Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.
• Chain: B
• Resolution: 2.805 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	rna	B	R119 N180	R119 N180

Gene Ontology

Molecular Function

• GO:0003674 molecular_function
• GO:0003723 RNA binding
• 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:0000956 nuclear-transcribed mRNA catabolic process
• GO:0006364 rRNA processing
• GO:0006396 RNA processing
• GO:0006401 RNA catabolic process
• GO:0016075 rRNA catabolic process
• GO:0034473 U1 snRNA 3'-end processing
• GO:0034475 U4 snRNA 3'-end processing
• GO:0034476 U5 snRNA 3'-end processing
• GO:0070478 nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay
• GO:0071028 nuclear mRNA surveillance
• GO:0071038 TRAMP-dependent tRNA surveillance pathway
• GO:0071039 nuclear polyadenylation-dependent CUT catabolic process
• 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:4ifd, PDBe:4ifd, PDBj:4ifd
• PDBsum: 4ifd
• PubMed: 23376952
• UniProt: P46948|RRP41_YEAST Exosome complex component SKI6 (Gene Name=SKI6)