Structure of PDB 6lqv Chain RK Binding Site BS01

Receptor Information

>6lqv Chain RK (length=360) Species: 559292 (Saccharomyces cerevisiae S288C)

KYTTFQGSQNFRLRIVLATLSGKPIKIEKIRSGDLNPGLKDYEVSFLRLI
ESVTNGSVIEISYTGTTVIYRPGIIVGGASTHICPSSKPVGYFVEPMLYL
APFSKKKFSILFKGITASHNDAGIEAIKWGLMPVMEKFGVRECALHTLKR
GSPPLGGGEVHLVVDSLIAQPITMHEIDRPIISSITGVAYSTRVSPSLVN
RMIDGAKKVLKNLQCEVNITADVWRGENSGKSPGWGITLVAQSKQKGWSY
FAEDIGDAGSIPEELGEKVACQLLEEISKSAAVGRNQLPLAIVYMVIGKE
DIGRLRINKEQIDERFIILLRDIKKIFNTEVFLKPVDEADNEDMIATIKG
IGFTNTSKKI

Ligand information

>6lqv Chain SA (length=950)

aagauaguuaucugguugauccugccaguagucauaugcuugucucagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaaggcucau
uaaaucaguuaucguuuauuugauaguuccaugguauaacugugguaauu
cuagagcuaauacaugcuaaucucgacccuuuggaagagauguauuuauu
agaucaaugucuucggacucuuugaugaaauaacuuuucgaaucgcaugg
ccuugugcuggcgaugguucauucaaauuucugcccuaucaacuuucgau
gguaggauaguggccuaccaugguuucaacggguaacggggaauaagggu
ucgauuccggagagggagccugagaaacggcuaccacauccaaggaaggc
agcaggccaaauuacccaauccuaauucagggagguagugacaauaaaua
acgauacagggcccauucgggucuuguaauuggaaugaguacaauguaaa
uaccuuaacgaggaacaauuggagggcaagucuggugccagcagccgcgg
uaauuccagcuccaauagcguauauuaaaguuguugcagcuggggggagu
auggucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccagg
aguggagccugcggcucaacacggggaaacucaccagguccagacacaau
aaggauugacauucuugauuuugugggugguggugcauugaugcccuugu
ucugggccacgcgcgcuacacugacggagccagcgagucuagugaaacuc
cgucgugcuggcaacgaggaauuccuaguaagcgcaagucaucagcuugc
guugauuacgucccugcccuuuguacacaccgcccgucgcuaguaccgau
ugaauggcuuagugaggcgacaaacuuggucauuuagaggaacuaaaagu

............................<<<<.<<<<<<........<<<
.<<...<<....<<....<<..........>>...>>.>>.....<<<..
.....<<<..<<..<<....<<<..........<.....<<.<<......
.>>.>>......>.......<<<<............>>>>.....<<<<<
...<<<<..............>>>>...>>>>>.........<<<<...<
<.....>>..>>>>....>>>...>>>>..>>>.<<<....<<<....<<
<<<<<<.......>>>>>>>>>>>......>>>.....<<..........
.....>>..>>>.<<.<<<..........>>>.>>.<.<<....>>.>..
..>>>>>......<<<....<<<.....>>>..>>>..............
.<<<<<<<.<<<<<....>>>>>.>>>.>>>>......<<..<.......
....>..>>.........<<<<<<.......<<<....>>>.........
.........>>>>>>..>>>>>>>>>>.........<....>........
............<<.........>>.....<<<<<<<<<<<<..<<.<<<
<<<..<<<.<<<<.......................<<.<....<<<<<.
.......<.....>......>>>>>......<<<........>>>...>.
>>.......>>>>.>>>.....<<<<<<<..................>>>
>>>>................>>>>>>....<<<<<<<<.......>>>>>
>>>......>>...>>>>>>>............>>>>>..<<<<.<<...
..<<<<<<<.<<<..<....>..>>>.>>>>>>>....>>.>>>>.....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6lqv Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.
• Resolution: 4.8 Å
• Binding residue (original residue number in PDB): R199 R231 G232
• Binding residue (residue number reindexed from 1): R193 R225 G226

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0003963 RNA-3'-phosphate cyclase activity
• GO:0004521 RNA endonuclease activity
• GO:0005515 protein binding
• GO:0008047 enzyme activator activity

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:0000479 endonucleolytic cleavage of tricistronic rRNA transcript (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:0006396 RNA processing
• GO:0030490 maturation of SSU-rRNA
• GO:0042254 ribosome biogenesis
• GO:0042274 ribosomal small subunit biogenesis
• GO:2000232 regulation of rRNA processing

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0030686 90S preribosome
• GO:0032040 small-subunit processome

External links

• PDB: RCSB:6lqv, PDBe:6lqv, PDBj:6lqv
• PDBsum: 6lqv
• PubMed: 32943522
• UniProt: Q08096|RCL1_YEAST RNA 3'-terminal phosphate cyclase-like protein (Gene Name=RCL1)