Structure of PDB 7v08 Chain v

Receptor sequence

>7v08v (length=293) Species: 1247190 (Saccharomyces cerevisiae BY4741)

NARAKRALVKREAKLVENVKQALFIPGQSCNKNLHDIMVDLSALKKPDMK
RFNRKNDIHPFEDMSPLEFFSEKNDCSLMVLMTSSKKRKNNMTFIRTFGY
KIYDMIELMVADNFKLLSDFKKLTFTVGLKPMFTFQGAAFDTHPVYKQIK
SLFLDFFRGESTDLQDVAGLQHVISMTIQGDFQDGEPLPNVLFRVYKLKS
YKSDQGGKRLPRIELVEIGPRLDFKIGRIHTPSPDMVTEAHKKPKQLEMK
TKKNVELDIMGDKLGRIHMGKQDLGKLQTRKMKGLKSKFDQGT

3D structure

• PDB: 7v08 rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly.
• Chain: v
• Resolution: 2.36 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	v	A10 R11 R14 F60 N61 R62 N64 P74 F77 F78 K81 N82 Q254 M257 K258 N262 L265 K271 R274 I275 H276 M277 G278 Q280 L282 Q286 R288 K289 K291 L293	A2 R3 R6 F52 N53 R54 N56 P66 F69 F70 K73 N74 Q246 M249 K250 N254 L257 K263 R266 I267 H268 M269 G270 Q272 L274 Q278 R280 K281 K283 L285
BS02	rna	v	N39 K40 H43 R59 S93 K94 K95 R96	N31 K32 H35 R51 S85 K86 K87 R88

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0008312 7S RNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000470 maturation of LSU-rRNA
• GO:0006364 rRNA processing
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

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

External links

• PDB: RCSB:7v08, PDBe:7v08, PDBj:7v08
• PDBsum: 7v08
• PubMed: 36864048
• UniProt: P36160|RPF2_YEAST Ribosome biogenesis protein RPF2 (Gene Name=RPF2)