Structure of PDB 7d63 Chain RH Binding Site BS01

Receptor Information
>7d63 Chain RH (length=230) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKALPASLVPQAPPVLTSKDKITKRMIVVLAMASLETHKISDKYVLLNCD
DHQGLLKKMGRDISEARPDITHQCLLTLLDSPINKAGKLQVYIQTSRGIL
IEVNPTVRIPRTFKRFSGLMVQLLHKLSIRSVNSEEKLLKVIKNPITDHL
PTKCRKVTLSFDAPVIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYV
DEKVGLSNYPLSASVACSKFCHGAEDAWNI
Ligand information
>7d63 Chain SA (length=1331) [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
uugccaaggacguuuucauuaaucaagaacgccgacuagggaucgggugg
uguuuuuuuaaugacccacucggcaccuuacgagacuggggggaguaugg
ucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccaggagug
gagccugcggcucaacacggggaaacucaccagguccagacacaauaagg
auugacauucuugauuuugugggugguggugcauugaugcccuuguucug
ggccacgcgcgcuacacugacggagccagcgagucuacccuuggccgaga
ggucuugggugaaacuccgucgugcuggggauagagcauuguaauuauug
cucuucaacgaggaauuccuaguaagcgcaagucaucagcuugcguugau
uacgucccugcccuuuguacacaccgcccgucgcuaguaccgauugaaug
gcuuagugaggccucaggaucugcuuagagaagggggcaacuccaucuca
gagcggagaauuuggacaaacuuggucauuuagaggaacuaaaaguuucc
guaggugaaccugcggaaggaucauuaaaga
............................<<<<.<<<<<<........<<<
.<<...<<....<<....<<..........>>...>>.>>.....<<<..
.....<<<..<<..<<....<<<..........<.....<<.<<......
.>>.>>......>.......<<<<............>>>>.....<<<<<
...<<<<..............>>>>...>>>>>.........<<<<...<
<.....>>..>>>>....>>>...>>>>..>>>.<<<....<<<....<<
<<<<<<.......>>>>>>>>>>>......>>>.....<<..........
.....>>..>>>.<<.<<<..........>>>.>>.<.<<....>>.>..
..>>>>>......<<<....<<<.....>>>..>>>..............
.<<<<<<<.<<<<<....>>>>>.>>>.>>>>......<<..<.......
....>..>>.........<<<<<<.......<<<....>>>.........
.........>>>>>>..>>>>>>>>>>.........<....<.<<...<<
<.<<..<<<<<.<<<<<..<.......>..>>>>>.>>>>>.<..<<..<
...>..>>.>....>>....<<<<<<.<<...<<<<..<<..<<<<<<.<
...<<<......>>>......>.>>>>>>..>>.......<<....>>..
.>>>>...>>>>>.>>>...>>>...>>.>..<<...<<<..<<<<<<<<
.<<<........>>>>>>>>>>>..>>>..>>.....>............
........<<.........>>.....<<<<<<<<<<<<..<<.<<<<<<.
.<<<.<<<<.......................<<.<....<<<<<.....
...<.....>......>>>>>......<<<........>>>...>.>>..
.....>>>>.>>>.....<<<<<<<.............<<..<<<<....
>>>>..>>......>>>>>>>...........<<<<<<..........>>
>>>>..........>>>>>>....<<<<<<<<.......>>>>>>>>...
...>>...>>>>>>>............>>>>>..<<<<.<<.....<<<<
<<<.<<<..<.<<......<<<<<<<...<<.<<<......>>>.>>...
>>>>>>>......>>.>..>>>.>>>>>>>....>>.>>>>.....<<<<
<<<<<....>>>>>>>>>.............
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7d63 Cryo-EM structure of 90S preribosome with inactive Utp24 (state C)
Resolution12.3 Å
Binding residue
(original residue number in PDB)		D63 D72 H73 Q74 L76 R88 I91 G119 L148 N165 A210 R211 S233 A234
Binding residue
(residue number reindexed from 1)		D42 D51 H52 Q53 L55 R67 I70 G98 L127 N144 A189 R190 S212 A213
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7d63, PDBe:7d63, PDBj:7d63
PDBsum7d63
PubMed
UniProtQ06287|NEP1_YEAST Ribosomal RNA small subunit methyltransferase NEP1 (Gene Name=EMG1)

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