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3OIN

Crystal structure of Saccharomyces cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA

Functional Information from GO Data
ChainGOidnamespacecontents
A0000447biological_processendonucleolytic 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)
A0000472biological_processendonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
A0000480biological_processendonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005730cellular_componentnucleolus
A0005737cellular_componentcytoplasm
A0005880cellular_componentnuclear microtubule
A0006364biological_processrRNA processing
A0008168molecular_functionmethyltransferase activity
A0019843molecular_functionrRNA binding
A0030490biological_processmaturation of SSU-rRNA
A0030686cellular_component90S preribosome
A0031167biological_processrRNA methylation
A0032040cellular_componentsmall-subunit processome
A0032259biological_processmethylation
A0034399cellular_componentnuclear periphery
A0042254biological_processribosome biogenesis
A0042274biological_processribosomal small subunit biogenesis
A0042802molecular_functionidentical protein binding
A0070037molecular_functionrRNA (pseudouridine) methyltransferase activity
A0070475biological_processrRNA base methylation
A1990904cellular_componentribonucleoprotein complex
B0000447biological_processendonucleolytic 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)
B0000472biological_processendonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
B0000480biological_processendonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005730cellular_componentnucleolus
B0005737cellular_componentcytoplasm
B0005880cellular_componentnuclear microtubule
B0006364biological_processrRNA processing
B0008168molecular_functionmethyltransferase activity
B0019843molecular_functionrRNA binding
B0030490biological_processmaturation of SSU-rRNA
B0030686cellular_component90S preribosome
B0031167biological_processrRNA methylation
B0032040cellular_componentsmall-subunit processome
B0032259biological_processmethylation
B0034399cellular_componentnuclear periphery
B0042254biological_processribosome biogenesis
B0042274biological_processribosomal small subunit biogenesis
B0042802molecular_functionidentical protein binding
B0070037molecular_functionrRNA (pseudouridine) methyltransferase activity
B0070475biological_processrRNA base methylation
B1990904cellular_componentribonucleoprotein complex
Functional Information from PDB Data
site_idAC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE GOL A 253
ChainResidue
ALYS39
AHOH265

site_idAC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL A 254
ChainResidue
AVAL162
ALYS164
AHOH284
AHOH313
BASP169
BHOH275
BHOH296

site_idAC3
Number of Residues15
DetailsBINDING SITE FOR RESIDUE SAH B 253
ChainResidue
BLEU180
BSER181
BPHE182
BGLY207
BMET209
BALA210
BARG211
BGLY212
BASP214
BGLY226
BLEU227
BSER228
BTYR230
BLEU232
BALA234

site_idAC4
Number of Residues10
DetailsBINDING SITE FOR RESIDUE SCY B 254
ChainResidue
BASN69
BASP71
BASP72
BHIS73
BGLN74
BLEU77
BILE84
BALA87
BHOH300
CC7

site_idAC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG C 15
ChainResidue
CG3
CHOH17
CHOH186
CHOH188
CHOH209
CHOH253

site_idAC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE CL C 16
ChainResidue
CG3

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:18063569, ECO:0000269|PubMed:21087996
ChainResidueDetails
ALEU180
AGLY207
AGLY212
ALEU227
BLEU180
BGLY207
BGLY212
BLEU227

site_idSWS_FT_FI2
Number of Residues8
DetailsSITE: Interaction with substrate rRNA => ECO:0000269|PubMed:21087996
ChainResidueDetails
AARG88
AARG129
AARG132
AARG136
BARG88
BARG129
BARG132
BARG136

site_idSWS_FT_FI3
Number of Residues2
DetailsSITE: Stabilizes Arg-88 => ECO:0000303|PubMed:21087996
ChainResidueDetails
AASP90
BASP90

221371

PDB entries from 2024-06-19

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