Structure of PDB 6ylx Chain b

Receptor sequence

>6ylxb (length=470) Species: 4932 (Saccharomyces cerevisiae)

MQLSWKDIPTVAPANDLLDIVLNRTQRKTPTVIRPGFKITRIRAFYMRKV
KYTGEGFVEKFEDILKGFPNINDVHPFHRDLMDTLYEKNHYKISLAAISR
AKSLVEQVARDYVRLLKFGQSLFQCKQLKRAALGRMATIVKKLRDPLAYL
EQVRQHIGRLPSIDPNTRTLLICGYPNVGKSSFLRCITKSDVDVQPYAFT
TKSLYVGHFDYKYLRFQAIDTPGILDRPTEEMNNIEMQSIYAIAHLRSCV
LYFMDLSEQCGFTIEAQVKLFHSIKPLFANKSVMVVINKTDIIRPEDLDE
ERAQLLESVKEVPGVEIMTSSCQLEENVMEVRNKACEKLLASRIENKLKS
QSRINNVLNKIHVAQPQARDDVKRTPFIPESVKNLKKYDPEDPNRRKLAR
DIEAENGGAGVFNVNLKDKYLLEDDEWKNDIMPEILDGKNVYDFLDPEIA
AKLQALEEEEEKLENEGFYN

3D structure

• PDB: 6ylx Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
• Chain: b
• Resolution: 3.9 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	D19 I20 L22 N23 Q26 R27 K28 T31 I33 R34 P35 G36 R48 K49 K51 N70 I71 K92 I93 L95 A96 R100 Q107 R110 F123 K126 K129 R130 A131 G134 R135 T138 R154 R159 S162 K189 Y197 F199 K202 V206 H208 R227 R400 G410 V411	D19 I20 L22 N23 Q26 R27 K28 T31 I33 R34 P35 G36 R48 K49 K51 N70 I71 K92 I93 L95 A96 R100 Q107 R110 F123 K126 K129 R130 A131 G134 R135 T138 R154 R159 S162 K189 Y197 F199 K202 V206 H208 R227 R400 G410 V411

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding

Biological Process

• GO:0000054 ribosomal subunit export from nucleus
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0030687 preribosome, large subunit precursor

External links

• PDB: RCSB:6ylx, PDBe:6ylx, PDBj:6ylx
• PDBsum: 6ylx
• PubMed: 32668200
• UniProt: Q02892|NOG1_YEAST Nucleolar GTP-binding protein 1 (Gene Name=NOG1)