Structure of PDB 8v83 Chain b

Receptor sequence

>8v83b (length=423) Species: 1247190 (Saccharomyces cerevisiae BY4741)

MQLSWKDIPTVAPANDLLDIVLNRTQRKTPTVIRPGFKITRIRAFYMRKV
KYTGEGFVEKFEDILKGFPNINDVHPFHRDLMDTLYEKNHYKISLAAISR
AKSLVEQVARDYVRLLKFGQSLFQCKQLKRAALGRMATIVKKLRDPLAYL
EQVRQHIGRLPSIDPNTRTLLICGYPNVGKSSFLRCITKSDVDVQPYAFT
TKSLYVGHFDYKYLRFQAIDTPGILDRPTEEMNNIEMQSIYAIAHLRSCV
LYFMDLSEQCGFTIEAQVKLFHSIKPLFANKSVMVVINKTLLESVKEVPG
VEIMTSSCQLEENVMEVRNKACEKLLARTPFIPESVKNLKKYDPEDPNRR
KLARDIEAENGGAGVFNVNLKDKYLLEDDEWKNDIMPEILDGKNVYDFLD
PEIAAKLQALEEEEEKLENEGFY

3D structure

• PDB: 8v83 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
• Chain: b
• Resolution: 2.53 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	K6 D19 I20 L22 N23 Q26 T31 V32 I33 R34 Y46 K49 P69 N70 I71 K92 L95 A96 S99 R100 S103 F123 K126 K129 R130 A131 G134 R135 Q155 R159 P161 S162 S190 Y197 F199 H208 R227 I235 G410 V411	K6 D19 I20 L22 N23 Q26 T31 V32 I33 R34 Y46 K49 P69 N70 I71 K92 L95 A96 S99 R100 S103 F123 K126 K129 R130 A131 G134 R135 Q155 R159 P161 S162 S190 Y197 F199 H208 R227 I235 G364 V365

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:8v83, PDBe:8v83, PDBj:8v83
• PDBsum: 8v83
• PubMed: 38632236
• UniProt: Q02892|NOG1_YEAST Nucleolar GTP-binding protein 1 (Gene Name=NOG1)