Structure of PDB 8pvk Chain Ce

Receptor sequence

>8pvkCe (length=313) Species: 759272 (Thermochaetoides thermophila DSM 1495)

VLKPLTGDNTEAPKQHSQPSRKGKKAWRKNIDLTEVEQGLEELNEQIIKG
GLKADEIIAQRSALPAVSVRKRAGTYDPWAPDPLKKPKTLEQKPISLAAN
GKSVPAVPKPTGGYSYNPAFTDYQQRLMEESEKAIEAERKRLQELELERQ
KMEAAARSAAEAEAAEARAEKPRRKTKAERNRIKRRKEEERKRKHEEAMK
RKQQQLEQAKKIAAEVEERERQLALQKIEEGDDTVLRRKQLGKFKLPEKD
LELVLPDELEDSLRRLKPEGNLLKDRYRSMIVRGKLEARRKIPFRKQAKT
KLTEKWTFKDFRI

3D structure

• PDB: 8pvk Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Chain: Ce
• Resolution: 2.55 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	Ce	P15 Q17 Q20 P21 S22 R23 K24 K26 K27 R30 K31 V103 R104 K105 R106 A107 P296 R297 R298 K299 A302 R304 N305 R306 R315 R343 K351 R368 K369 K373 R419 R420 K421 I422 P423 F424 R425 K426 A428 K429 L432 W436 K439 D440	P13 Q15 Q18 P19 S20 R21 K22 K24 K25 R28 K29 V69 R70 K71 R72 A73 P172 R173 R174 K175 A178 R180 N181 R182 R191 R219 K227 R238 K239 K243 R289 R290 K291 I292 P293 F294 R295 K296 A298 K299 L302 W306 K309 D310
BS02	rna	Ce	P180 P182 K184 T188 E434 K435 W436	P81 P83 K85 T89 E304 K305 W306
BS03	rna	Ce	K87 I91	K53 I57

Gene Ontology

Molecular Function

• GO:0008097 5S rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006364 rRNA processing
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus

External links

• PDB: RCSB:8pvk, PDBe:8pvk, PDBj:8pvk
• PDBsum: 8pvk
• PubMed: 37921038
• UniProt: G0S495