Structure of PDB 6lqp Chain 5K

Receptor sequence

>6lqp5K (length=175) Species: 559292 (Saccharomyces cerevisiae S288C)

TRKFGLVKRTLNTKKDQRLKKNQENLTRNIPQVSSALFFQYNQAIKPPYQ
VLIDTNFINFSIQKKVDIVRGMMDCLLAKCNPLITDCVMAELEKLGPKYR
IALKLARDPRIKRLSCSHKGTYADDCLVHRVLQHKCYIVATNDAGLKQRI
RKIPGIPLMSVGGHAYVIEKLPDVF

3D structure

• PDB: 6lqp Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.
• Chain: 5K
• Resolution: 3.2 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	5K	Q23 K133 G134	Q17 K119 G120
BS02	rna	5K	V13 K14 K21	V7 K8 K15
BS03	rna	5K	R42 I44 Q162 R163 K166	R28 I30 Q148 R149 K152
BS04	ZN	5K	C101 C130 H132 C140	C87 C116 H118 C126

Gene Ontology

Molecular Function

• GO:0004521 RNA endonuclease activity
• GO:0004540 RNA nuclease activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding

Biological Process

• GO:0000447 endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000472 endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000480 endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0030490 maturation of SSU-rRNA
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0032040 small-subunit processome

External links

• PDB: RCSB:6lqp, PDBe:6lqp, PDBj:6lqp
• PDBsum: 6lqp
• PubMed: 32943522
• UniProt: Q05498|FCF1_YEAST rRNA-processing protein FCF1 (Gene Name=FCF1)