Structure of PDB 8v87 Chain j

Receptor sequence

>8v87j (length=73) Species: 1247190 (Saccharomyces cerevisiae BY4741)

KSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKAKRRHTTGTGR
MRYLKHVSRRFKNGFQTGSASKA

3D structure

• PDB: 8v87 The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis.
• Chain: j
• Resolution: 2.66 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	j	H16 R24 H28 S35 K43 T44 R45 Y47 N48 W49 K52 R55 R56	H3 R11 H15 S22 K30 T31 R32 Y34 N35 W36 K39 R42 R43
BS02	rna	j	R21 A42 T59 T61 G62 R63 M64 R65 Y66 L67 K68 R72 F74 N76 Q79 G81 S82 A83 K85 A86	R8 A29 T46 T48 G49 R50 M51 R52 Y53 L54 K55 R59 F61 N63 Q66 G68 S69 A70 K72 A73
BS03	ZN	j	C19 C22 C34 C37	C6 C9 C21 C24

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030687 preribosome, large subunit precursor
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8v87, PDBe:8v87, PDBj:8v87
• PDBsum: 8v87
• PubMed: 38632236
• UniProt: P49166|RL37A_YEAST Large ribosomal subunit protein eL37A (Gene Name=RPL37A)