Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7R72

State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 local model

Functional Information from GO Data

Chain	GOid	namespace	contents
8	0003729	molecular_function	mRNA binding
8	0005515	molecular_function	protein binding
8	0005634	cellular_component	nucleus
8	0005654	cellular_component	nucleoplasm
8	0005730	cellular_component	nucleolus
8	0005739	cellular_component	mitochondrion
8	0030687	cellular_component	preribosome, large subunit precursor
8	0030690	cellular_component	Noc1p-Noc2p complex
8	0030691	cellular_component	Noc2p-Noc3p complex
8	0042254	biological_process	ribosome biogenesis
8	0042273	biological_process	ribosomal large subunit biogenesis
b	0000054	biological_process	ribosomal subunit export from nucleus
b	0000166	molecular_function	nucleotide binding
b	0003723	molecular_function	RNA binding
b	0003924	molecular_function	GTPase activity
b	0005515	molecular_function	protein binding
b	0005525	molecular_function	GTP binding
b	0005730	cellular_component	nucleolus
b	0005737	cellular_component	cytoplasm
b	0006364	biological_process	rRNA processing
b	0030687	cellular_component	preribosome, large subunit precursor
b	0042254	biological_process	ribosome biogenesis
b	0042273	biological_process	ribosomal large subunit biogenesis
b	1902626	biological_process	assembly of large subunit precursor of preribosome
B	0000027	biological_process	ribosomal large subunit assembly
B	0002181	biological_process	cytoplasmic translation
B	0003723	molecular_function	RNA binding
B	0003735	molecular_function	structural constituent of ribosome
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005840	cellular_component	ribosome
B	0006364	biological_process	rRNA processing
B	0006412	biological_process	translation
B	0006414	biological_process	translational elongation
B	0022625	cellular_component	cytosolic large ribosomal subunit
B	1990145	biological_process	maintenance of translational fidelity
B	1990904	cellular_component	ribonucleoprotein complex
c	0002181	biological_process	cytoplasmic translation
c	0003723	molecular_function	RNA binding
c	0003735	molecular_function	structural constituent of ribosome
c	0005737	cellular_component	cytoplasm
c	0005829	cellular_component	cytosol
c	0005840	cellular_component	ribosome
c	0006364	biological_process	rRNA processing
c	0022625	cellular_component	cytosolic large ribosomal subunit
c	0030627	molecular_function	pre-mRNA 5'-splice site binding
c	0048025	biological_process	negative regulation of mRNA splicing, via spliceosome
c	1990904	cellular_component	ribonucleoprotein complex
d	0002181	biological_process	cytoplasmic translation
d	0003735	molecular_function	structural constituent of ribosome
d	0005737	cellular_component	cytoplasm
d	0005829	cellular_component	cytosol
d	0005840	cellular_component	ribosome
d	0006412	biological_process	translation
d	0006450	biological_process	regulation of translational fidelity
d	0022625	cellular_component	cytosolic large ribosomal subunit
d	1990904	cellular_component	ribonucleoprotein complex
g	0002181	biological_process	cytoplasmic translation
g	0003735	molecular_function	structural constituent of ribosome
g	0005737	cellular_component	cytoplasm
g	0005829	cellular_component	cytosol
g	0005840	cellular_component	ribosome
g	0006412	biological_process	translation
g	0022625	cellular_component	cytosolic large ribosomal subunit
g	0030687	cellular_component	preribosome, large subunit precursor
g	0042254	biological_process	ribosome biogenesis
g	1990904	cellular_component	ribonucleoprotein complex
G	0000470	biological_process	maturation of LSU-rRNA
G	0002181	biological_process	cytoplasmic translation
G	0003723	molecular_function	RNA binding
G	0003735	molecular_function	structural constituent of ribosome
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0005840	cellular_component	ribosome
G	0006364	biological_process	rRNA processing
G	0022625	cellular_component	cytosolic large ribosomal subunit
G	0042254	biological_process	ribosome biogenesis
G	1990904	cellular_component	ribonucleoprotein complex
I	0003682	molecular_function	chromatin binding
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005656	cellular_component	nuclear pre-replicative complex
I	0005730	cellular_component	nucleolus
I	0006260	biological_process	DNA replication
I	0006267	biological_process	pre-replicative complex assembly involved in nuclear cell cycle DNA replication
I	0006270	biological_process	DNA replication initiation
I	0006364	biological_process	rRNA processing
I	0030691	cellular_component	Noc2p-Noc3p complex
I	0042254	biological_process	ribosome biogenesis
I	0042273	biological_process	ribosomal large subunit biogenesis
I	0051301	biological_process	cell division
j	0000448	biological_process	cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
j	0002181	biological_process	cytoplasmic translation
j	0003723	molecular_function	RNA binding
j	0003735	molecular_function	structural constituent of ribosome
j	0005515	molecular_function	protein binding
j	0005737	cellular_component	cytoplasm
j	0005829	cellular_component	cytosol
j	0005840	cellular_component	ribosome
j	0006412	biological_process	translation
j	0008270	molecular_function	zinc ion binding
j	0019843	molecular_function	rRNA binding
j	0022625	cellular_component	cytosolic large ribosomal subunit
j	0030687	cellular_component	preribosome, large subunit precursor
j	0046872	molecular_function	metal ion binding
j	1990904	cellular_component	ribonucleoprotein complex
k	0002181	biological_process	cytoplasmic translation
k	0003735	molecular_function	structural constituent of ribosome
k	0005515	molecular_function	protein binding
k	0005737	cellular_component	cytoplasm
k	0005829	cellular_component	cytosol
k	0005840	cellular_component	ribosome
k	0006412	biological_process	translation
k	0022618	biological_process	protein-RNA complex assembly
k	0022625	cellular_component	cytosolic large ribosomal subunit
k	1990904	cellular_component	ribonucleoprotein complex
m	0006364	biological_process	rRNA processing
m	0042254	biological_process	ribosome biogenesis
n	0005730	cellular_component	nucleolus
n	0042254	biological_process	ribosome biogenesis
p	0000463	biological_process	maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
p	0000466	biological_process	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
p	0003674	molecular_function	molecular_function
p	0005515	molecular_function	protein binding
p	0005634	cellular_component	nucleus
p	0005654	cellular_component	nucleoplasm
p	0005730	cellular_component	nucleolus
p	0006364	biological_process	rRNA processing
p	0030687	cellular_component	preribosome, large subunit precursor
p	0042254	biological_process	ribosome biogenesis
p	0042273	biological_process	ribosomal large subunit biogenesis
p	0043021	molecular_function	ribonucleoprotein complex binding
p	0051276	biological_process	chromosome organization
p	0070545	cellular_component	PeBoW complex
p	0110136	biological_process	protein-RNA complex remodeling
P	0000448	biological_process	cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
P	0002181	biological_process	cytoplasmic translation
P	0003735	molecular_function	structural constituent of ribosome
P	0005737	cellular_component	cytoplasm
P	0005829	cellular_component	cytosol
P	0005840	cellular_component	ribosome
P	0006412	biological_process	translation
P	0015934	cellular_component	large ribosomal subunit
P	0022625	cellular_component	cytosolic large ribosomal subunit
P	0030687	cellular_component	preribosome, large subunit precursor
P	1990904	cellular_component	ribonucleoprotein complex
R	0002181	biological_process	cytoplasmic translation
R	0003723	molecular_function	RNA binding
R	0003735	molecular_function	structural constituent of ribosome
R	0005737	cellular_component	cytoplasm
R	0005829	cellular_component	cytosol
R	0005840	cellular_component	ribosome
R	0006412	biological_process	translation
R	0015934	cellular_component	large ribosomal subunit
R	0022625	cellular_component	cytosolic large ribosomal subunit
R	0022626	cellular_component	cytosolic ribosome
R	1990904	cellular_component	ribonucleoprotein complex
t	0000463	biological_process	maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
t	0000465	biological_process	exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
t	0003723	molecular_function	RNA binding
t	0003729	molecular_function	mRNA binding
t	0003735	molecular_function	structural constituent of ribosome
t	0005515	molecular_function	protein binding
t	0005730	cellular_component	nucleolus
t	0022625	cellular_component	cytosolic large ribosomal subunit
t	0030687	cellular_component	preribosome, large subunit precursor
t	0042134	molecular_function	rRNA primary transcript binding
t	0042254	biological_process	ribosome biogenesis
t	0042273	biological_process	ribosomal large subunit biogenesis
u	0001671	molecular_function	ATPase activator activity
u	0003735	molecular_function	structural constituent of ribosome
u	0005634	cellular_component	nucleus
u	0005730	cellular_component	nucleolus
u	0005737	cellular_component	cytoplasm
u	0030687	cellular_component	preribosome, large subunit precursor
u	0032781	biological_process	positive regulation of ATP-dependent activity
u	0042254	biological_process	ribosome biogenesis
u	0042273	biological_process	ribosomal large subunit biogenesis
u	0051117	molecular_function	ATPase binding
u	1902626	biological_process	assembly of large subunit precursor of preribosome
U	0002181	biological_process	cytoplasmic translation
U	0003723	molecular_function	RNA binding
U	0003735	molecular_function	structural constituent of ribosome
U	0005515	molecular_function	protein binding
U	0005737	cellular_component	cytoplasm
U	0005829	cellular_component	cytosol
U	0005840	cellular_component	ribosome
U	0006412	biological_process	translation
U	0022625	cellular_component	cytosolic large ribosomal subunit
U	1990904	cellular_component	ribonucleoprotein complex
w	0000451	biological_process	rRNA 2'-O-methylation
w	0000463	biological_process	maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
w	0000466	biological_process	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
w	0001510	biological_process	RNA methylation
w	0005515	molecular_function	protein binding
w	0005634	cellular_component	nucleus
w	0005730	cellular_component	nucleolus
w	0006364	biological_process	rRNA processing
w	0008168	molecular_function	methyltransferase activity
w	0008649	molecular_function	rRNA methyltransferase activity
w	0008650	molecular_function	rRNA (uridine-2'-O-)-methyltransferase activity
w	0016435	molecular_function	rRNA (guanine) methyltransferase activity
w	0016740	molecular_function	transferase activity
w	0030687	cellular_component	preribosome, large subunit precursor
w	0031167	biological_process	rRNA methylation
w	0032259	biological_process	methylation
w	0042254	biological_process	ribosome biogenesis
w	0070039	molecular_function	rRNA (guanosine-2'-O-)-methyltransferase activity
x	0000027	biological_process	ribosomal large subunit assembly
x	0000166	molecular_function	nucleotide binding
x	0000470	biological_process	maturation of LSU-rRNA
x	0003676	molecular_function	nucleic acid binding
x	0003723	molecular_function	RNA binding
x	0003724	molecular_function	RNA helicase activity
x	0004386	molecular_function	helicase activity
x	0005515	molecular_function	protein binding
x	0005524	molecular_function	ATP binding
x	0005654	cellular_component	nucleoplasm
x	0005730	cellular_component	nucleolus
x	0006364	biological_process	rRNA processing
x	0016787	molecular_function	hydrolase activity
x	0016887	molecular_function	ATP hydrolysis activity
x	0030686	cellular_component	90S preribosome
x	0030687	cellular_component	preribosome, large subunit precursor
x	0042254	biological_process	ribosome biogenesis
x	0070013	cellular_component	intracellular organelle lumen
x	1902626	biological_process	assembly of large subunit precursor of preribosome
X	0000027	biological_process	ribosomal large subunit assembly
X	0002181	biological_process	cytoplasmic translation
X	0003723	molecular_function	RNA binding
X	0003735	molecular_function	structural constituent of ribosome
X	0005515	molecular_function	protein binding
X	0005737	cellular_component	cytoplasm
X	0005829	cellular_component	cytosol
X	0005840	cellular_component	ribosome
X	0006412	biological_process	translation
X	0019843	molecular_function	rRNA binding
X	0022625	cellular_component	cytosolic large ribosomal subunit
X	0030687	cellular_component	preribosome, large subunit precursor
X	1990904	cellular_component	ribonucleoprotein complex
Z	0002181	biological_process	cytoplasmic translation
Z	0003735	molecular_function	structural constituent of ribosome
Z	0005737	cellular_component	cytoplasm
Z	0005829	cellular_component	cytosol
Z	0005840	cellular_component	ribosome
Z	0006412	biological_process	translation
Z	0022625	cellular_component	cytosolic large ribosomal subunit
Z	1990904	cellular_component	ribonucleoprotein complex

Functional Information from PROSITE/UniProt

site_id	PS00039
Number of Residues	9
Details	DEAD_ATP_HELICASE DEAD-box subfamily ATP-dependent helicases signature. VMDEADRlL

Chain	Residue	Details
x	VAL170-LEU178

site_id	PS00050
Number of Residues	16
Details	RIBOSOMAL_L23 Ribosomal protein L23 signature. KKAYVRLTadydaldI

Chain	Residue	Details
X	LYS120-ILE135

site_id	PS00464
Number of Residues	25
Details	RIBOSOMAL_L22 Ribosomal protein L22 signature. RrrTyRAhGRinkyesspSHIELvV

Chain	Residue	Details
P	ARG126-VAL150

site_id	PS00474
Number of Residues	24
Details	RIBOSOMAL_L3 Ribosomal protein L3 signature. FeqnemiDaiAvTkGHGfeGvthR

Chain	Residue	Details
B	PHE209-ARG232

site_id	PS00526
Number of Residues	20
Details	RIBOSOMAL_L19E Ribosomal protein L19e signature. QKRLaAsvvgVGkrkVWLDP

Chain	Residue	Details
R	GLN7-PRO26

site_id	PS00634
Number of Residues	33
Details	RIBOSOMAL_L30 Ribosomal protein L30 signature. ILslLrLvEtnTgVfvkltknvypLLkvIapYV

Chain	Residue	Details
t	ILE162-VAL194

site_id	PS00678
Number of Residues	15
Details	WD_REPEATS_1 Trp-Asp (WD) repeats signature. LATGsdDgTVRVWEI

Chain	Residue	Details
m	LEU452-ILE466
p	ILE118-LEU132
p	LEU391-VAL405

site_id	PS00709
Number of Residues	25
Details	RIBOSOMAL_L30E_1 Ribosomal protein L30e signature 1. SgkytlGyKstVKslRqGksKlIII

Chain	Residue	Details
c	SER20-ILE44

site_id	PS00993
Number of Residues	21
Details	RIBOSOMAL_L30E_2 Ribosomal protein L30e signature 2. ELGTavGKlfrvgvVsIlEaG

Chain	Residue	Details
c	GLU76-GLY96

site_id	PS01077
Number of Residues	20
Details	RIBOSOMAL_L37E Ribosomal protein L37e signature. GTpSfGkRhnks.HtlCnRCG

Chain	Residue	Details
j	GLY4-GLY23

site_id	PS01082
Number of Residues	18
Details	RIBOSOMAL_L7AE Ribosomal protein L7Ae signature. CkkmgVPYaiVkGKarLG

Chain	Residue	Details
G	CYS170-GLY187

site_id	PS01107
Number of Residues	12
Details	RIBOSOMAL_L27E Ribosomal protein L27e signature. GKNqWFFskLRF

Chain	Residue	Details
Z	GLY125-PHE136

site_id	PS01144
Number of Residues	15
Details	RIBOSOMAL_L31E Ribosomal protein L31e signature. VRLApeLNqAiWkRG

Chain	Residue	Details
d	VAL49-GLY63

site_id	PS01145
Number of Residues	14
Details	RIBOSOMAL_L34E Ribosomal protein L34e signature. TrSnKikvvKTPGG

Chain	Residue	Details
g	THR15-GLY28

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	13
Details	Compositional bias: {"description":"Basic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	45
Details	Coiled coil: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	9
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)","evidences":[{"source":"PubMed","id":"15542864","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	18
Details	Zinc finger: {"description":"C4-type","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22096102","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	39
Details	Repeat: {"description":"WD 1","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	40
Details	Repeat: {"description":"WD 2","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	42
Details	Repeat: {"description":"WD 3","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	38
Details	Repeat: {"description":"WD 4","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	39
Details	Repeat: {"description":"WD 5","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	39
Details	Repeat: {"description":"WD 6","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	31
Details	Repeat: {"description":"WD 7","evidences":[{"source":"HAMAP-Rule","id":"MF_03027","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	39
Details	Repeat: {"description":"WD 1","evidences":[{"source":"HAMAP-Rule","id":"MF_03029","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	38
Details	Repeat: {"description":"WD 3","evidences":[{"source":"HAMAP-Rule","id":"MF_03029","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	40
Details	Repeat: {"description":"WD 4","evidences":[{"source":"HAMAP-Rule","id":"MF_03029","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	40
Details	Repeat: {"description":"WD 6","evidences":[{"source":"HAMAP-Rule","id":"MF_03029","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	29
Details	Coiled coil: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03163","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	12
Details	Compositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	186
Details	Domain: {"description":"Helicase ATP-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	28
Details	Motif: {"description":"Q motif","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI26
Number of Residues	3
Details	Motif: {"description":"DEAD box","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI27
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI28
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)