Structure of PDB 7d5s Chain RH Binding Site BS01

Receptor Information

>7d5s Chain RH (length=230) Species: 559292 (Saccharomyces cerevisiae S288C)

QKALPASLVPQAPPVLTSKDKITKRMIVVLAMASLETHKISDKYVLLNCD
DHQGLLKKMGRDISEARPDITHQCLLTLLDSPINKAGKLQVYIQTSRGIL
IEVNPTVRIPRTFKRFSGLMVQLLHKLSIRSVNSEEKLLKVIKNPITDHL
PTKCRKVTLSFDAPVIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYV
DEKVGLSNYPLSASVACSKFCHGAEDAWNI

Ligand information

>7d5s Chain SA (length=859)

aagauaguuaucugguugauccugccaguagucauaugcuugucucacaa
auuagugacaauaaauaacgauacagggcccauucgggucuuguaauugg
aaugaguacaauguaaauaccuuaacgaggaacaauuggagggcaagucu
ggugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguug
uugcaggcucguaguugaacuuagggacggucgggggcaucaguauucaa
uugucagaggugaaauucuuggauuuauugaagacuaacuacugcgaaag
cauuugccaaggacguuuucauuaaucaagaacgaaaguuaggggaucga
agaugaucagauaccgucguagucuuaacuggggggaguauggucgcaag
gcugaaacuuaaaggaauugacggaagggcaccaccaggaguggagccug
cggcucaacacggggaaacucaccagguccagacacaauaaggauugaca
uucuugauuuugugggugguggugcauugaugcccuuguucugggccacg
cgcgcuacacugacggagccagcgagucuaaccuuggccgagaggucuug
guaaucuugugaaacuccgucgugcuggggauauucaacgaggaauuccu
aguaagcgcaagucaucagcuugcguugauuacgucccugcccuuuguac
acaccgcccgucgcuaguaccgauugaauggcuuagugaggccucaggau
cugcuuagagaagggggcaacuccaucucagagcggagaauuuggacaaa
cuuggucauuuagaggaacuaaaagucguaacaagguuuccguaggugaa
ccugcggaa

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7d5s Cryo-EM structure of 90S preribosome with inactive Utp24 (state A2)
• Resolution: 4.6 Å
• Binding residue (original residue number in PDB): D63 D72 H73 Q74 L76 R88 I91 G119 L148 R151 S155 K158 N165 A210 R211 S233 A234
• Binding residue (residue number reindexed from 1): D42 D51 H52 Q53 L55 R67 I70 G98 L127 R130 S134 K137 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

External links

• PDB: RCSB:7d5s, PDBe:7d5s, PDBj:7d5s
• PDBsum: 7d5s
• UniProt: Q06287|NEP1_YEAST Ribosomal RNA small subunit methyltransferase NEP1 (Gene Name=EMG1)