Structure of PDB 6lqq Chain RG Binding Site BS01

Receptor Information
>6lqq Chain RG (length=216) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVLTSKDKITKRMIVVLAMASLETHKIDKYVLLNCDDHQGLLKKMGRDIS
EARPDITHQCLLTLLDSPINKAGKLQVYIQTSRGILIEVNPTVRIPRTFK
RFSGLMVQLLHKLSIRSVNSEEKLLKVIKNPITDHLPTKCRKVTLSFDAP
VIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYVDEKVGLSNYPLSAS
VACSKFCHGAEDAWNI
Ligand information
>6lqq Chain SA (length=1323) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aagauaguuaucugguugauccugccaguagucauaugcuugucucagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaaggcucau
uaaaucaguuaucguuuauuugauaguuccaugguauaacugugguaauu
cuagagcuaauacaugcuaaucucgacccuuuggaagagauguauuuauu
agaucaaugucuucggacucuuugaugaaauaacuuuucgaaucgcaugg
ccuugugcuggcgaugguucauucaaauuucugcccuaucaacuuucgau
gguaggauaguggccuaccaugguuucaacggguaacggggaauaagggu
ucgauuccggagagggagccugagaaacggcuaccacauccaaggaaggc
agcaggccaaauuacccaauccuaauucagggagguagugacaauaaaua
acgauacagggcccauucgggucuuguaauuggaaugaguacaauguaaa
uaccuuaacgaggaacaauuggagggcaagucuggugccagcagccgcgg
uaauuccagcuccaauagcguauauuaaaguuguugcagaagcucguagu
ugaacuggcccgguuggccgguccggauuuccaacggggccuugguucua
uuuucuaggacugauuaauagggacggucgggggcaucaguauucaauug
ucagaggugaaauucuuggauuuauugaagacuaacuacugcgaaagcau
uugccaaggacguuuucauuaaucaagaacgaccauaaacuaugccgacu
agggaucgggugguguuuuuuuaaugacccacucggcaccuuacgagaac
uggggggaguauggucgcaaggcugaaacuuaaaggaauugacggaaggg
caccaccaggaguggagccugcggcucaacacggggaaacucaccagguc
cagacacaauaaggauugacauucuugauuuugugggugguggugcauug
augcccuuguucugggccacgcgcgcuacacugacggagccagcgagucu
aaccuuggccgagaggucuugguaaucuugugaaacuccgucgugcuggc
aacgaggaauuccuaguaagcgcaagucaucagcuugcguugauuacguc
ccugcccuuuguacacaccgcccgucgcuaguaccgauugaauggcuuag
ugaggccucaggaucugcuuagagaagggggcaacuccaucucagagcgg
agaauuuggacaaacuuggucauuuagaggaacuaaaagucguaacaagg
uuuccguaggugaaccugcggaa
............................<<<<.<<<<<<........<<<
.<<...<<....<<....<<..........>>...>>.>>.....<<<..
.....<<<..<<..<<....<<<..........<.....<<.<<......
.>>.>>......>.......<<<<............>>>>.....<<<<<
...<<<<..............>>>>...>>>>>.........<<<<...<
<.....>>..>>>>....>>>...>>>>..>>>.<<<....<<<....<<
<<<<<<.......>>>>>>>>>>>......>>>.....<<..........
.....>>..>>>.<<.<<<..........>>>.>>.<.<<....>>.>..
..>>>>>......<<<....<<<.....>>>..>>>..............
.<<<<<<<.<<<<<....>>>>>.>>>.>>>>......<<..<.......
....>..>>.........<<<<<<.......<<<....>>>.........
.........>>>>>>..>>>>>>>>>>.........<....<.<<...<<
<.<<..<<<<<.<<<<<..<.......>..>>>>>.>>>>>.<..<<..<
...>..>>.>....>>....<<<<<<.<<...<<<<..<<..<<<<<<.<
...<<<......>>>......>.>>>>>>..>>.......<<....>>..
.>>>>...>>>>>.>>>...>>>...>>.>...............<<...
<<<..<<<<<<<<.<<<........>>>>>>>>>>>..>>>..>>.....
.>....................<<.........>>.....<<<<<<<<<<
<<..<<.<<<<<<..<<<.<<<<.......................<<.<
....<<<<<........<.....>......>>>>>......<<<......
..>>>...>.>>.......>>>>.>>>.....<<<<<<<...........
.<<<..<<<<....>>>>..>>>............>>>>>>>........
........>>>>>>....<<<<<<<<.......>>>>>>>>......>>.
..>>>>>>>............>>>>>..<<<<.<<.....<<<<<<<.<<
<..<.<<......<<<<<<<...<<.<<<......>>>.>>...>>>>>>
>......>>.>..>>>.>>>>>>>....>>.>>>>...............
.<<<<<<<<<....>>>>>>>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6lqq Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.
Resolution4.1 Å
Binding residue
(original residue number in PDB)		R129 P131 R132 R136 G139 V142 I150 V153 L159
Binding residue
(residue number reindexed from 1)		R94 P96 R97 R101 G104 V107 I115 V118 L124
Enzymatic activity
Enzyme Commision number 2.1.1.260: rRNA small subunit pseudouridine methyltransferase Nep1.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0019843 rRNA binding
GO:0042802 identical protein binding
GO:0070037 rRNA (pseudouridine) methyltransferase 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: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:0031167 rRNA methylation
GO:0032259 methylation
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
GO:0070475 rRNA base methylation
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005880 nuclear microtubule
GO:0030686 90S preribosome
GO:0032040 small-subunit processome
GO:0034399 nuclear periphery
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6lqq, PDBe:6lqq, PDBj:6lqq
PDBsum6lqq
PubMed32943522
UniProtQ06287|NEP1_YEAST Ribosomal RNA small subunit methyltransferase NEP1 (Gene Name=EMG1)

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