Structure of PDB 7d63 Chain RH

Receptor sequence
>7d63RH (length=230) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
QKALPASLVPQAPPVLTSKDKITKRMIVVLAMASLETHKISDKYVLLNCD
DHQGLLKKMGRDISEARPDITHQCLLTLLDSPINKAGKLQVYIQTSRGIL
IEVNPTVRIPRTFKRFSGLMVQLLHKLSIRSVNSEEKLLKVIKNPITDHL
PTKCRKVTLSFDAPVIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYV
DEKVGLSNYPLSASVACSKFCHGAEDAWNI
3D structure
PDB7d63 Cryo-EM structure of 90S preribosome with inactive Utp24 (state C)
ChainRH
Resolution12.3 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.1.1.260: rRNA small subunit pseudouridine methyltransferase Nep1.
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 RH D63 D72 H73 Q74 L76 R88 I91 G119 L148 N165 A210 R211 S233 A234 D42 D51 H52 Q53 L55 R67 I70 G98 L127 N144 A189 R190 S212 A213
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
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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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