Structure of PDB 4ifd Chain A

Receptor sequence

>4ifdA (length=300) Species: 559292 (Saccharomyces cerevisiae S288C)

AKDIEISASESKFILEALRQNYRLDGRSFDQFRDVEITFGKEFGDVSVKM
GNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDE
VLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDAS
CIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPVPLGILHIPICVTFSFF
NPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKNREVVQVSKA
GGLPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRNKYAAMLTSEN

3D structure

• PDB: 4ifd Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.
• Chain: A
• 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	A	Y68 D70	Y67 D69

Gene Ontology

Molecular Function

• GO:0003674 molecular_function
• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0035925 mRNA 3'-UTR AU-rich region 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:0034473 U1 snRNA 3'-end processing
• GO:0034475 U4 snRNA 3'-end processing
• GO:0034476 U5 snRNA 3'-end processing
• GO:0071028 nuclear mRNA surveillance
• GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process
• GO:0071038 TRAMP-dependent tRNA surveillance pathway

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: Q05636|RRP45_YEAST Exosome complex component RRP45 (Gene Name=RRP45)