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7NAD

State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model

Functional Information from GO Data
ChainGOidnamespacecontents
50000477biological_processgeneration of mature 5'-end of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
50004534molecular_function5'-3' RNA exonuclease activity
50005515molecular_functionprotein binding
50005634cellular_componentnucleus
50005730cellular_componentnucleolus
50005737cellular_componentcytoplasm
50006364biological_processrRNA processing
50019843molecular_functionrRNA binding
50034399cellular_componentnuclear periphery
50042254biological_processribosome biogenesis
51990275molecular_functionpreribosome binding
80003729molecular_functionmRNA binding
80005515molecular_functionprotein binding
80005634cellular_componentnucleus
80005654cellular_componentnucleoplasm
80005730cellular_componentnucleolus
80005739cellular_componentmitochondrion
80030687cellular_componentpreribosome, large subunit precursor
80030690cellular_componentNoc1p-Noc2p complex
80030691cellular_componentNoc2p-Noc3p complex
80042254biological_processribosome biogenesis
80042273biological_processribosomal large subunit biogenesis
B0000027biological_processribosomal large subunit assembly
B0002181biological_processcytoplasmic translation
B0003723molecular_functionRNA binding
B0003735molecular_functionstructural constituent of ribosome
B0005515molecular_functionprotein binding
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0005840cellular_componentribosome
B0006364biological_processrRNA processing
B0006412biological_processtranslation
B0006414biological_processtranslational elongation
B0022625cellular_componentcytosolic large ribosomal subunit
B1990145biological_processmaintenance of translational fidelity
B1990904cellular_componentribonucleoprotein complex
G0000470biological_processmaturation of LSU-rRNA
G0002181biological_processcytoplasmic translation
G0003723molecular_functionRNA binding
G0003735molecular_functionstructural constituent of ribosome
G0005737cellular_componentcytoplasm
G0005829cellular_componentcytosol
G0005840cellular_componentribosome
G0006364biological_processrRNA processing
G0022625cellular_componentcytosolic large ribosomal subunit
G0042254biological_processribosome biogenesis
G1990904cellular_componentribonucleoprotein complex
I0003682molecular_functionchromatin binding
I0005515molecular_functionprotein binding
I0005634cellular_componentnucleus
I0005654cellular_componentnucleoplasm
I0005656cellular_componentnuclear pre-replicative complex
I0005730cellular_componentnucleolus
I0006260biological_processDNA replication
I0006267biological_processpre-replicative complex assembly involved in nuclear cell cycle DNA replication
I0006270biological_processDNA replication initiation
I0006364biological_processrRNA processing
I0030691cellular_componentNoc2p-Noc3p complex
I0042254biological_processribosome biogenesis
I0042273biological_processribosomal large subunit biogenesis
I0051301biological_processcell division
P0000448biological_processcleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
P0002181biological_processcytoplasmic translation
P0003735molecular_functionstructural constituent of ribosome
P0005737cellular_componentcytoplasm
P0005829cellular_componentcytosol
P0005840cellular_componentribosome
P0006412biological_processtranslation
P0015934cellular_componentlarge ribosomal subunit
P0022625cellular_componentcytosolic large ribosomal subunit
P0030687cellular_componentpreribosome, large subunit precursor
P1990904cellular_componentribonucleoprotein complex
R0002181biological_processcytoplasmic translation
R0003723molecular_functionRNA binding
R0003735molecular_functionstructural constituent of ribosome
R0005737cellular_componentcytoplasm
R0005829cellular_componentcytosol
R0005840cellular_componentribosome
R0006412biological_processtranslation
R0015934cellular_componentlarge ribosomal subunit
R0022625cellular_componentcytosolic large ribosomal subunit
R0022626cellular_componentcytosolic ribosome
R1990904cellular_componentribonucleoprotein complex
U0002181biological_processcytoplasmic translation
U0003723molecular_functionRNA binding
U0003735molecular_functionstructural constituent of ribosome
U0005737cellular_componentcytoplasm
U0005829cellular_componentcytosol
U0005840cellular_componentribosome
U0006412biological_processtranslation
U0022625cellular_componentcytosolic large ribosomal subunit
U1990904cellular_componentribonucleoprotein complex
X0000027biological_processribosomal large subunit assembly
X0002181biological_processcytoplasmic translation
X0003723molecular_functionRNA binding
X0003735molecular_functionstructural constituent of ribosome
X0005515molecular_functionprotein binding
X0005737cellular_componentcytoplasm
X0005829cellular_componentcytosol
X0005840cellular_componentribosome
X0006412biological_processtranslation
X0019843molecular_functionrRNA binding
X0022625cellular_componentcytosolic large ribosomal subunit
X0030687cellular_componentpreribosome, large subunit precursor
X1990904cellular_componentribonucleoprotein complex
Z0002181biological_processcytoplasmic translation
Z0003735molecular_functionstructural constituent of ribosome
Z0005737cellular_componentcytoplasm
Z0005829cellular_componentcytosol
Z0005840cellular_componentribosome
Z0006412biological_processtranslation
Z0022625cellular_componentcytosolic large ribosomal subunit
Z1990904cellular_componentribonucleoprotein complex
b0000054biological_processribosomal subunit export from nucleus
b0000166molecular_functionnucleotide binding
b0003723molecular_functionRNA binding
b0003924molecular_functionGTPase activity
b0005515molecular_functionprotein binding
b0005525molecular_functionGTP binding
b0005634cellular_componentnucleus
b0005730cellular_componentnucleolus
b0005737cellular_componentcytoplasm
b0006364biological_processrRNA processing
b0030687cellular_componentpreribosome, large subunit precursor
b0042254biological_processribosome biogenesis
b0042273biological_processribosomal large subunit biogenesis
b1902626biological_processassembly of large subunit precursor of preribosome
c0002181biological_processcytoplasmic translation
c0003723molecular_functionRNA binding
c0003735molecular_functionstructural constituent of ribosome
c0005737cellular_componentcytoplasm
c0005829cellular_componentcytosol
c0005840cellular_componentribosome
c0006364biological_processrRNA processing
c0022625cellular_componentcytosolic large ribosomal subunit
c0030627molecular_functionpre-mRNA 5'-splice site binding
c0048025biological_processnegative regulation of mRNA splicing, via spliceosome
c1990904cellular_componentribonucleoprotein complex
d0002181biological_processcytoplasmic translation
d0003735molecular_functionstructural constituent of ribosome
d0005737cellular_componentcytoplasm
d0005829cellular_componentcytosol
d0005840cellular_componentribosome
d0006412biological_processtranslation
d0006450biological_processregulation of translational fidelity
d0022625cellular_componentcytosolic large ribosomal subunit
d1990904cellular_componentribonucleoprotein complex
g0002181biological_processcytoplasmic translation
g0003735molecular_functionstructural constituent of ribosome
g0005737cellular_componentcytoplasm
g0005829cellular_componentcytosol
g0005840cellular_componentribosome
g0006412biological_processtranslation
g0022625cellular_componentcytosolic large ribosomal subunit
g0030687cellular_componentpreribosome, large subunit precursor
g0042254biological_processribosome biogenesis
g1990904cellular_componentribonucleoprotein complex
j0000448biological_processcleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
j0002181biological_processcytoplasmic translation
j0003723molecular_functionRNA binding
j0003735molecular_functionstructural constituent of ribosome
j0005737cellular_componentcytoplasm
j0005829cellular_componentcytosol
j0005840cellular_componentribosome
j0006412biological_processtranslation
j0008270molecular_functionzinc ion binding
j0019843molecular_functionrRNA binding
j0022625cellular_componentcytosolic large ribosomal subunit
j0030687cellular_componentpreribosome, large subunit precursor
j0044391cellular_componentribosomal subunit
j0046872molecular_functionmetal ion binding
j1990904cellular_componentribonucleoprotein complex
k0002181biological_processcytoplasmic translation
k0003735molecular_functionstructural constituent of ribosome
k0005737cellular_componentcytoplasm
k0005829cellular_componentcytosol
k0005840cellular_componentribosome
k0006412biological_processtranslation
k0022618biological_processprotein-RNA complex assembly
k0022625cellular_componentcytosolic large ribosomal subunit
k1990904cellular_componentribonucleoprotein complex
m0006364biological_processrRNA processing
m0042254biological_processribosome biogenesis
n0005730cellular_componentnucleolus
n0042254biological_processribosome biogenesis
p0000463biological_processmaturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
p0000466biological_processmaturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
p0003674molecular_functionmolecular_function
p0005515molecular_functionprotein binding
p0005634cellular_componentnucleus
p0005654cellular_componentnucleoplasm
p0005730cellular_componentnucleolus
p0006364biological_processrRNA processing
p0030687cellular_componentpreribosome, large subunit precursor
p0042254biological_processribosome biogenesis
p0042273biological_processribosomal large subunit biogenesis
p0043021molecular_functionribonucleoprotein complex binding
p0051276biological_processchromosome organization
p0070545cellular_componentPeBoW complex
p0110136biological_processprotein-RNA complex remodeling
t0000463biological_processmaturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
t0000465biological_processexonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
t0003723molecular_functionRNA binding
t0003729molecular_functionmRNA binding
t0003735molecular_functionstructural constituent of ribosome
t0005515molecular_functionprotein binding
t0005634cellular_componentnucleus
t0005730cellular_componentnucleolus
t0022625cellular_componentcytosolic large ribosomal subunit
t0030687cellular_componentpreribosome, large subunit precursor
t0042134molecular_functionrRNA primary transcript binding
t0042254biological_processribosome biogenesis
t0042273biological_processribosomal large subunit biogenesis
u0001671molecular_functionATPase activator activity
u0003735molecular_functionstructural constituent of ribosome
u0005634cellular_componentnucleus
u0005730cellular_componentnucleolus
u0005737cellular_componentcytoplasm
u0030687cellular_componentpreribosome, large subunit precursor
u0032781biological_processpositive regulation of ATP-dependent activity
u0042254biological_processribosome biogenesis
u0042273biological_processribosomal large subunit biogenesis
u0051117molecular_functionATPase binding
u1902626biological_processassembly of large subunit precursor of preribosome
w0000451biological_processrRNA 2'-O-methylation
w0000463biological_processmaturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
w0000466biological_processmaturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
w0001510biological_processRNA methylation
w0005515molecular_functionprotein binding
w0005634cellular_componentnucleus
w0005730cellular_componentnucleolus
w0006364biological_processrRNA processing
w0008168molecular_functionmethyltransferase activity
w0008649molecular_functionrRNA methyltransferase activity
w0008650molecular_functionrRNA (uridine-2'-O-)-methyltransferase activity
w0016435molecular_functionrRNA (guanine) methyltransferase activity
w0016740molecular_functiontransferase activity
w0030687cellular_componentpreribosome, large subunit precursor
w0031167biological_processrRNA methylation
w0032259biological_processmethylation
w0042254biological_processribosome biogenesis
w0070039molecular_functionrRNA (guanosine-2'-O-)-methyltransferase activity
x0000027biological_processribosomal large subunit assembly
x0000166molecular_functionnucleotide binding
x0000470biological_processmaturation of LSU-rRNA
x0003676molecular_functionnucleic acid binding
x0003723molecular_functionRNA binding
x0003724molecular_functionRNA helicase activity
x0004386molecular_functionhelicase activity
x0005515molecular_functionprotein binding
x0005524molecular_functionATP binding
x0005634cellular_componentnucleus
x0005654cellular_componentnucleoplasm
x0005730cellular_componentnucleolus
x0006364biological_processrRNA processing
x0016787molecular_functionhydrolase activity
x0016887molecular_functionATP hydrolysis activity
x0030686cellular_component90S preribosome
x0030687cellular_componentpreribosome, large subunit precursor
x0042254biological_processribosome biogenesis
x0070013cellular_componentintracellular organelle lumen
x1902626biological_processassembly of large subunit precursor of preribosome
Functional Information from PROSITE/UniProt
site_idPS00039
Number of Residues9
DetailsDEAD_ATP_HELICASE DEAD-box subfamily ATP-dependent helicases signature. VMDEADRlL
ChainResidueDetails
xVAL170-LEU178

site_idPS00050
Number of Residues16
DetailsRIBOSOMAL_L23 Ribosomal protein L23 signature. KKAYVRLTadydaldI
ChainResidueDetails
XLYS120-ILE135

site_idPS00464
Number of Residues25
DetailsRIBOSOMAL_L22 Ribosomal protein L22 signature. RrrTyRAhGRinkyesspSHIELvV
ChainResidueDetails
PARG126-VAL150

site_idPS00474
Number of Residues24
DetailsRIBOSOMAL_L3 Ribosomal protein L3 signature. FeqnemiDaiAvTkGHGfeGvthR
ChainResidueDetails
BPHE209-ARG232

site_idPS00526
Number of Residues20
DetailsRIBOSOMAL_L19E Ribosomal protein L19e signature. QKRLaAsvvgVGkrkVWLDP
ChainResidueDetails
RGLN7-PRO26

site_idPS00634
Number of Residues33
DetailsRIBOSOMAL_L30 Ribosomal protein L30 signature. ILslLrLvEtnTgVfvkltknvypLLkvIapYV
ChainResidueDetails
tILE162-VAL194

site_idPS00678
Number of Residues15
DetailsWD_REPEATS_1 Trp-Asp (WD) repeats signature. IISGsyDgIVRTWDL
ChainResidueDetails
pILE118-LEU132
pLEU391-VAL405
mLEU452-ILE466

site_idPS00709
Number of Residues25
DetailsRIBOSOMAL_L30E_1 Ribosomal protein L30e signature 1. SgkytlGyKstVKslRqGksKlIII
ChainResidueDetails
cSER20-ILE44

site_idPS00993
Number of Residues21
DetailsRIBOSOMAL_L30E_2 Ribosomal protein L30e signature 2. ELGTavGKlfrvgvVsIlEaG
ChainResidueDetails
cGLU76-GLY96

site_idPS01077
Number of Residues20
DetailsRIBOSOMAL_L37E Ribosomal protein L37e signature. GTpSfGkRhnks.HtlCnRCG
ChainResidueDetails
jGLY4-GLY23

site_idPS01082
Number of Residues18
DetailsRIBOSOMAL_L7AE Ribosomal protein L7Ae signature. CkkmgVPYaiVkGKarLG
ChainResidueDetails
GCYS170-GLY187

site_idPS01107
Number of Residues12
DetailsRIBOSOMAL_L27E Ribosomal protein L27e signature. GKNqWFFskLRF
ChainResidueDetails
ZGLY125-PHE136

site_idPS01144
Number of Residues15
DetailsRIBOSOMAL_L31E Ribosomal protein L31e signature. VRLApeLNqAiWkRG
ChainResidueDetails
dVAL49-GLY63

site_idPS01145
Number of Residues14
DetailsRIBOSOMAL_L34E Ribosomal protein L34e signature. TrSnKikvvKTPGG
ChainResidueDetails
gTHR15-GLY28

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues13
DetailsCompositional bias: {"description":"Basic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues45
DetailsCoiled coil: {"evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues9
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)","evidences":[{"source":"PubMed","id":"15542864","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues39
DetailsRepeat: {"description":"WD 1","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues40
DetailsRepeat: {"description":"WD 2","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues42
DetailsRepeat: {"description":"WD 3","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues38
DetailsRepeat: {"description":"WD 4","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues39
DetailsRepeat: {"description":"WD 5","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI12
Number of Residues39
DetailsRepeat: {"description":"WD 6","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI13
Number of Residues31
DetailsRepeat: {"description":"WD 7","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI14
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI15
Number of Residues39
DetailsRepeat: {"description":"WD 1","evidences":[{"source":"HAMAP-Rule","id":"MF_03029","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI16
Number of Residues38
DetailsRepeat: {"description":"WD 3","evidences":[{"source":"HAMAP-Rule","id":"MF_03029","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI17
Number of Residues40
DetailsRepeat: {"description":"WD 4","evidences":[{"source":"HAMAP-Rule","id":"MF_03029","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI18
Number of Residues40
DetailsRepeat: {"description":"WD 6","evidences":[{"source":"HAMAP-Rule","id":"MF_03029","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI19
Number of Residues29
DetailsCoiled coil: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03163","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI20
Number of Residues12
DetailsCompositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}
ChainResidueDetails

site_idSWS_FT_FI21
Number of Residues1
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_03163","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI22
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03163","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI23
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI24
Number of Residues18
DetailsZinc finger: {"description":"C4-type","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI25
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22096102","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI26
Number of Residues186
DetailsDomain: {"description":"Helicase ATP-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI27
Number of Residues28
DetailsMotif: {"description":"Q motif","evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI28
Number of Residues3
DetailsMotif: {"description":"DEAD box","evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI29
Number of Residues7
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI30
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

238895

PDB entries from 2025-07-16

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