Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2NN6

Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000178	cellular_component	exosome (RNase complex)
A	0006396	biological_process	RNA processing
B	0000175	molecular_function	3'-5'-RNA exonuclease activity
B	0000176	cellular_component	nuclear exosome (RNase complex)
B	0000177	cellular_component	cytoplasmic exosome (RNase complex)
B	0000178	cellular_component	exosome (RNase complex)
B	0000460	biological_process	maturation of 5.8S rRNA
B	0000791	cellular_component	euchromatin
B	0000956	biological_process	nuclear-transcribed mRNA catabolic process
B	0003723	molecular_function	RNA binding
B	0004532	molecular_function	RNA exonuclease activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005730	cellular_component	nucleolus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006364	biological_process	rRNA processing
B	0006396	biological_process	RNA processing
B	0006401	biological_process	RNA catabolic process
B	0016075	biological_process	rRNA catabolic process
B	0030307	biological_process	positive regulation of cell growth
B	0034475	biological_process	U4 snRNA 3'-end processing
B	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
B	0045006	biological_process	DNA deamination
B	0051607	biological_process	defense response to virus
B	0071028	biological_process	nuclear mRNA surveillance
B	0071044	biological_process	histone mRNA catabolic process
B	0071051	biological_process	poly(A)-dependent snoRNA 3'-end processing
B	0101019	cellular_component	nucleolar exosome (RNase complex)
B	1905354	cellular_component	exoribonuclease complex
C	0000176	cellular_component	nuclear exosome (RNase complex)
C	0000177	cellular_component	cytoplasmic exosome (RNase complex)
C	0000178	cellular_component	exosome (RNase complex)
C	0000467	biological_process	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
C	0001650	cellular_component	fibrillar center
C	0003723	molecular_function	RNA binding
C	0004532	molecular_function	RNA exonuclease activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005730	cellular_component	nucleolus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006364	biological_process	rRNA processing
C	0006396	biological_process	RNA processing
C	0006401	biological_process	RNA catabolic process
C	0016075	biological_process	rRNA catabolic process
C	0034473	biological_process	U1 snRNA 3'-end processing
C	0034475	biological_process	U4 snRNA 3'-end processing
C	0034476	biological_process	U5 snRNA 3'-end processing
C	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
C	0042802	molecular_function	identical protein binding
C	0071028	biological_process	nuclear mRNA surveillance
C	0071035	biological_process	nuclear polyadenylation-dependent rRNA catabolic process
C	0071038	biological_process	TRAMP-dependent tRNA surveillance pathway
C	0101019	cellular_component	nucleolar exosome (RNase complex)
C	1905354	cellular_component	exoribonuclease complex
D	0000175	molecular_function	3'-5'-RNA exonuclease activity
D	0000176	cellular_component	nuclear exosome (RNase complex)
D	0000177	cellular_component	cytoplasmic exosome (RNase complex)
D	0000178	cellular_component	exosome (RNase complex)
D	0000791	cellular_component	euchromatin
D	0003677	molecular_function	DNA binding
D	0003723	molecular_function	RNA binding
D	0004532	molecular_function	RNA exonuclease activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005730	cellular_component	nucleolus
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006364	biological_process	rRNA processing
D	0006396	biological_process	RNA processing
D	0006401	biological_process	RNA catabolic process
D	0006402	biological_process	mRNA catabolic process
D	0016075	biological_process	rRNA catabolic process
D	0034475	biological_process	U4 snRNA 3'-end processing
D	0045006	biological_process	DNA deamination
D	0051607	biological_process	defense response to virus
D	0071028	biological_process	nuclear mRNA surveillance
D	0071051	biological_process	poly(A)-dependent snoRNA 3'-end processing
D	0101019	cellular_component	nucleolar exosome (RNase complex)
D	1905354	cellular_component	exoribonuclease complex
E	0000175	molecular_function	3'-5'-RNA exonuclease activity
E	0000176	cellular_component	nuclear exosome (RNase complex)
E	0000177	cellular_component	cytoplasmic exosome (RNase complex)
E	0000178	cellular_component	exosome (RNase complex)
E	0000467	biological_process	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
E	0003723	molecular_function	RNA binding
E	0004532	molecular_function	RNA exonuclease activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005730	cellular_component	nucleolus
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006364	biological_process	rRNA processing
E	0006396	biological_process	RNA processing
E	0006401	biological_process	RNA catabolic process
E	0016075	biological_process	rRNA catabolic process
E	0016607	cellular_component	nuclear speck
E	0034473	biological_process	U1 snRNA 3'-end processing
E	0034475	biological_process	U4 snRNA 3'-end processing
E	0034476	biological_process	U5 snRNA 3'-end processing
E	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
E	0071028	biological_process	nuclear mRNA surveillance
E	0071035	biological_process	nuclear polyadenylation-dependent rRNA catabolic process
E	0071038	biological_process	TRAMP-dependent tRNA surveillance pathway
E	0101019	cellular_component	nucleolar exosome (RNase complex)
E	1905354	cellular_component	exoribonuclease complex
F	0000176	cellular_component	nuclear exosome (RNase complex)
F	0000177	cellular_component	cytoplasmic exosome (RNase complex)
F	0000178	cellular_component	exosome (RNase complex)
F	0003723	molecular_function	RNA binding
F	0004532	molecular_function	RNA exonuclease activity
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005730	cellular_component	nucleolus
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006259	biological_process	DNA metabolic process
F	0006364	biological_process	rRNA processing
F	0006396	biological_process	RNA processing
F	0006401	biological_process	RNA catabolic process
F	0016075	biological_process	rRNA catabolic process
F	0034475	biological_process	U4 snRNA 3'-end processing
F	0045006	biological_process	DNA deamination
F	0045190	biological_process	isotype switching
F	0071028	biological_process	nuclear mRNA surveillance
F	0071051	biological_process	poly(A)-dependent snoRNA 3'-end processing
F	0101019	cellular_component	nucleolar exosome (RNase complex)
G	0000175	molecular_function	3'-5'-RNA exonuclease activity
G	0000176	cellular_component	nuclear exosome (RNase complex)
G	0000177	cellular_component	cytoplasmic exosome (RNase complex)
G	0000178	cellular_component	exosome (RNase complex)
G	0000467	biological_process	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
G	0000791	cellular_component	euchromatin
G	0000956	biological_process	nuclear-transcribed mRNA catabolic process
G	0003723	molecular_function	RNA binding
G	0004532	molecular_function	RNA exonuclease activity
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005730	cellular_component	nucleolus
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0006259	biological_process	DNA metabolic process
G	0006364	biological_process	rRNA processing
G	0006396	biological_process	RNA processing
G	0006401	biological_process	RNA catabolic process
G	0006402	biological_process	mRNA catabolic process
G	0010467	biological_process	gene expression
G	0010468	biological_process	regulation of gene expression
G	0034475	biological_process	U4 snRNA 3'-end processing
G	0045006	biological_process	DNA deamination
G	0045190	biological_process	isotype switching
G	0071034	biological_process	CUT catabolic process
G	0071035	biological_process	nuclear polyadenylation-dependent rRNA catabolic process
G	0071038	biological_process	TRAMP-dependent tRNA surveillance pathway
G	0071051	biological_process	poly(A)-dependent snoRNA 3'-end processing
G	0101019	cellular_component	nucleolar exosome (RNase complex)
H	0000175	molecular_function	3'-5'-RNA exonuclease activity
H	0000176	cellular_component	nuclear exosome (RNase complex)
H	0000177	cellular_component	cytoplasmic exosome (RNase complex)
H	0000178	cellular_component	exosome (RNase complex)
H	0000467	biological_process	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
H	0000956	biological_process	nuclear-transcribed mRNA catabolic process
H	0003723	molecular_function	RNA binding
H	0004532	molecular_function	RNA exonuclease activity
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005730	cellular_component	nucleolus
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006364	biological_process	rRNA processing
H	0006396	biological_process	RNA processing
H	0006401	biological_process	RNA catabolic process
H	0008312	molecular_function	7S RNA binding
H	0030307	biological_process	positive regulation of cell growth
H	0034475	biological_process	U4 snRNA 3'-end processing
H	0071034	biological_process	CUT catabolic process
H	0071035	biological_process	nuclear polyadenylation-dependent rRNA catabolic process
H	0071038	biological_process	TRAMP-dependent tRNA surveillance pathway
H	0071051	biological_process	poly(A)-dependent snoRNA 3'-end processing
H	0101019	cellular_component	nucleolar exosome (RNase complex)
I	0000176	cellular_component	nuclear exosome (RNase complex)
I	0000177	cellular_component	cytoplasmic exosome (RNase complex)
I	0000178	cellular_component	exosome (RNase complex)
I	0003676	molecular_function	nucleic acid binding
I	0003723	molecular_function	RNA binding
I	0004532	molecular_function	RNA exonuclease activity
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005730	cellular_component	nucleolus
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0006364	biological_process	rRNA processing
I	0006396	biological_process	RNA processing
I	0006401	biological_process	RNA catabolic process
I	0101019	cellular_component	nucleolar exosome (RNase complex)

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	267
Details	Region: {"description":"ARE binding","evidences":[{"source":"PubMed","id":"16912217","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"25218447","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"25755297","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"25772364","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","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 SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	81
Details	Domain: {"description":"S1 motif"}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18691976","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)