Structure of PDB 8qca Chain B

Receptor sequence

>8qcaB (length=756) Species: 4932 (Saccharomyces cerevisiae)

YTAAKYITETYASKPNWQAASSIASRLIKGEKAKAELRSNNWPFRVVGIA
HLEKQEESDSIEWFQSALRVDPNDVESWVGLGQAYHACGRIEASIKVFDK
AIQLRPSHTFAQYFKAISLCDVGEYLESLDILEKVCQEAATEESFQIGLV
EVLMRCSLDLYSQGFLLKSVSIAKDTIERIKIIISELKCENQQVWIYLSQ
VLRLFIWIESKVDTLPVESLVSIFENSEEIDSVDNIKIDTLLDSTTDDNV
SIACKFLILASKYSGTVRASYWYNIGISELTAFITLKEPQYRDAAIFAFK
KSIQLQSNTSETWIGLGIATMDINFRVSQHCFIKATALEPKATNTWFNLA
MLGLKKKDTEFAQQVLNKLQSLAPQDSSPWLGMALILEEQGDIIGSSKLF
AHSFILSNGRSKAAQFMYAKNVLENHINNGDDERDIETVEKLTTASIALE
QFFKKSPDSQFALQCALLTLERLHHYENANELANRLIGILEKKFEKTQDE
RELFNFAIIKGQFARIHLGLGNFELSIENADLSQGIISESSDEKSMKTKI
SNHICLGLSYFFLNDFDQTLNQFQELLSISKDSKHLVVLIAKVLYDVGES
DTKEIALQELTEYIATSGADLLVTLTIAAMSILDDKREDLSIILEELKAL
PLSKQIIDKHKDAPYLIEEITKRLYRNDTGKQVWQRSAYFFPNNLKVWER
LDKNIQRRIASNGQNKVTAEEMSKLYCESKNLRSIQRGMFLCPWNVTAVK
ALNECF

3D structure

• PDB: 8qca Concerted structural rearrangements enable RNA channeling into the cytoplasmic Ski238-Ski7-exosome assembly.
• Chain: B
• Resolution: 2.84 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	B	V882 L908 N915 F1170 F1182 G1211	V221 L242 N249 F494 F506 G535

Gene Ontology

Molecular Function

• GO:0003674 molecular_function
• GO:0005515 protein binding

Biological Process

• GO:0000956 nuclear-transcribed mRNA catabolic process
• GO:0006401 RNA catabolic process
• GO:0006402 mRNA catabolic process
• GO:0051607 defense response to virus
• GO:0070478 nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay
• GO:0070481 nuclear-transcribed mRNA catabolic process, non-stop decay

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0055087 Ski complex

External links

• PDB: RCSB:8qca, PDBe:8qca, PDBj:8qca
• PDBsum: 8qca
• PubMed: 37879335
• UniProt: P17883|SKI3_YEAST Superkiller protein 3 (Gene Name=SKI3)