Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4IFD

Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000176	cellular_component	nuclear exosome (RNase complex)
A	0000177	cellular_component	cytoplasmic exosome (RNase complex)
A	0000178	cellular_component	exosome (RNase complex)
A	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)
A	0003674	molecular_function	molecular_function
A	0003723	molecular_function	RNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005730	cellular_component	nucleolus
A	0005737	cellular_component	cytoplasm
A	0006364	biological_process	rRNA processing
A	0006396	biological_process	RNA processing
A	0006401	biological_process	RNA catabolic process
A	0016075	biological_process	rRNA catabolic process
A	0034473	biological_process	U1 snRNA 3'-end processing
A	0034475	biological_process	U4 snRNA 3'-end processing
A	0034476	biological_process	U5 snRNA 3'-end processing
A	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
A	0071028	biological_process	nuclear mRNA surveillance
A	0071035	biological_process	nuclear polyadenylation-dependent rRNA catabolic process
A	0071038	biological_process	TRAMP-dependent tRNA surveillance pathway
B	0000176	cellular_component	nuclear exosome (RNase complex)
B	0000177	cellular_component	cytoplasmic exosome (RNase complex)
B	0000178	cellular_component	exosome (RNase complex)
B	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)
B	0000956	biological_process	nuclear-transcribed mRNA catabolic process
B	0003674	molecular_function	molecular_function
B	0003723	molecular_function	RNA binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005730	cellular_component	nucleolus
B	0005737	cellular_component	cytoplasm
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	0034473	biological_process	U1 snRNA 3'-end processing
B	0034475	biological_process	U4 snRNA 3'-end processing
B	0034476	biological_process	U5 snRNA 3'-end processing
B	0070478	biological_process	nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay
B	0071028	biological_process	nuclear mRNA surveillance
B	0071038	biological_process	TRAMP-dependent tRNA surveillance pathway
B	0071039	biological_process	nuclear polyadenylation-dependent CUT catabolic process
B	0071051	biological_process	poly(A)-dependent snoRNA 3'-end processing
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	0000956	biological_process	nuclear-transcribed mRNA catabolic process
C	0003674	molecular_function	molecular_function
C	0003723	molecular_function	RNA binding
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	0006364	biological_process	rRNA processing
C	0006396	biological_process	RNA processing
C	0006397	biological_process	mRNA processing
C	0006401	biological_process	RNA catabolic process
C	0006402	biological_process	mRNA catabolic process
C	0016072	biological_process	rRNA metabolic 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	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	0071042	biological_process	nuclear polyadenylation-dependent mRNA catabolic process
D	0000176	cellular_component	nuclear exosome (RNase complex)
D	0000177	cellular_component	cytoplasmic exosome (RNase complex)
D	0000178	cellular_component	exosome (RNase complex)
D	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)
D	0003674	molecular_function	molecular_function
D	0003723	molecular_function	RNA binding
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005730	cellular_component	nucleolus
D	0005737	cellular_component	cytoplasm
D	0006364	biological_process	rRNA processing
D	0006396	biological_process	RNA processing
D	0006401	biological_process	RNA catabolic process
D	0016075	biological_process	rRNA catabolic process
D	0034475	biological_process	U4 snRNA 3'-end processing
D	0071028	biological_process	nuclear mRNA surveillance
D	0071035	biological_process	nuclear polyadenylation-dependent rRNA catabolic process
D	0071038	biological_process	TRAMP-dependent tRNA surveillance pathway
D	0071042	biological_process	nuclear polyadenylation-dependent mRNA catabolic process
D	0071051	biological_process	poly(A)-dependent snoRNA 3'-end processing
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	0003674	molecular_function	molecular_function
E	0003723	molecular_function	RNA binding
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005730	cellular_component	nucleolus
E	0005737	cellular_component	cytoplasm
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	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
F	0000176	cellular_component	nuclear exosome (RNase complex)
F	0000177	cellular_component	cytoplasmic exosome (RNase complex)
F	0000178	cellular_component	exosome (RNase complex)
F	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)
F	0003674	molecular_function	molecular_function
F	0003723	molecular_function	RNA binding
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005730	cellular_component	nucleolus
F	0005737	cellular_component	cytoplasm
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	0071028	biological_process	nuclear mRNA surveillance
F	0071035	biological_process	nuclear polyadenylation-dependent rRNA catabolic process
F	0071038	biological_process	TRAMP-dependent tRNA surveillance pathway
F	0071039	biological_process	nuclear polyadenylation-dependent CUT catabolic process
F	0071051	biological_process	poly(A)-dependent snoRNA 3'-end processing
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	0000956	biological_process	nuclear-transcribed mRNA catabolic process
G	0003723	molecular_function	RNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005730	cellular_component	nucleolus
G	0005737	cellular_component	cytoplasm
G	0006364	biological_process	rRNA processing
G	0006396	biological_process	RNA processing
G	0006401	biological_process	RNA catabolic process
G	0030145	molecular_function	manganese ion binding
G	0034475	biological_process	U4 snRNA 3'-end processing
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
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	0003674	molecular_function	molecular_function
H	0003723	molecular_function	RNA binding
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005730	cellular_component	nucleolus
H	0005737	cellular_component	cytoplasm
H	0006364	biological_process	rRNA processing
H	0006396	biological_process	RNA processing
H	0006401	biological_process	RNA catabolic process
H	0034475	biological_process	U4 snRNA 3'-end processing
H	0071028	biological_process	nuclear mRNA surveillance
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
I	0000176	cellular_component	nuclear exosome (RNase complex)
I	0000177	cellular_component	cytoplasmic exosome (RNase complex)
I	0000178	cellular_component	exosome (RNase complex)
I	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)
I	0000956	biological_process	nuclear-transcribed mRNA catabolic process
I	0003674	molecular_function	molecular_function
I	0003723	molecular_function	RNA binding
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005730	cellular_component	nucleolus
I	0005737	cellular_component	cytoplasm
I	0006364	biological_process	rRNA processing
I	0006396	biological_process	RNA processing
I	0006397	biological_process	mRNA processing
I	0006401	biological_process	RNA catabolic process
I	0070481	biological_process	nuclear-transcribed mRNA catabolic process, non-stop decay
I	0071035	biological_process	nuclear polyadenylation-dependent rRNA catabolic process
I	0071038	biological_process	TRAMP-dependent tRNA surveillance pathway
J	0000049	molecular_function	tRNA binding
J	0000175	molecular_function	3'-5'-RNA exonuclease activity
J	0000176	cellular_component	nuclear exosome (RNase complex)
J	0000177	cellular_component	cytoplasmic exosome (RNase complex)
J	0000178	cellular_component	exosome (RNase complex)
J	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)
J	0003676	molecular_function	nucleic acid binding
J	0003723	molecular_function	RNA binding
J	0004518	molecular_function	nuclease activity
J	0004519	molecular_function	endonuclease activity
J	0004521	molecular_function	RNA endonuclease activity
J	0004527	molecular_function	exonuclease activity
J	0004540	molecular_function	RNA nuclease activity
J	0005515	molecular_function	protein binding
J	0005634	cellular_component	nucleus
J	0005730	cellular_component	nucleolus
J	0005737	cellular_component	cytoplasm
J	0005739	cellular_component	mitochondrion
J	0006364	biological_process	rRNA processing
J	0006396	biological_process	RNA processing
J	0006397	biological_process	mRNA processing
J	0006401	biological_process	RNA catabolic process
J	0016075	biological_process	rRNA catabolic process
J	0016787	molecular_function	hydrolase activity
J	0043628	biological_process	regulatory ncRNA 3'-end processing
J	0070651	biological_process	nonfunctional rRNA decay
J	0071028	biological_process	nuclear mRNA surveillance
J	0071031	biological_process	nuclear mRNA surveillance of mRNA 3'-end processing
J	0071034	biological_process	CUT catabolic process
J	0071035	biological_process	nuclear polyadenylation-dependent rRNA catabolic process
J	0071038	biological_process	TRAMP-dependent tRNA surveillance pathway
J	0071039	biological_process	nuclear polyadenylation-dependent CUT catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE BR A 401

Chain	Residue
A	THR224

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE BR A 402

Chain	Residue
A	ARG71
A	PRO72
A	PHE73
A	GLU74

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL C 401

Chain	Residue
C	ILE54
C	GLU55
C	ASN56
C	PHE392

site_id	AC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE BR E 301

Chain	Residue
E	TRP217

site_id	AC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE BR F 301

Chain	Residue
F	GLY11

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL G 301

Chain	Residue
A	ASP26
G	ARG209
G	GLN230
G	GLU233

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MES G 302

Chain	Residue
G	ASP152
G	GLY153
G	LYS197
G	CYS198
G	GLU199
G	LEU201
G	THR204

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE BR H 401

Chain	Residue
H	LYS131
H	GLN132

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL H 402

Chain	Residue
H	TYR104
H	ALA105
H	SER204
H	ILE207
H	ARG209
H	VAL227

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL H 403

Chain	Residue
H	ARG115
H	ASP127
H	GLN201
H	TYR230

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL H 404

Chain	Residue
B	MET113
H	HIS71
H	GLY72
H	THR73
H	SER83

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE BR I 301

Chain	Residue
I	SER212
I	ALA248
I	ARG249

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE BR J 1101

Chain	Residue
J	PRO293
J	ARG294

site_id	BC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE BR J 1102

Chain	Residue
J	MET606

site_id	BC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE BR J 1103

Chain	Residue
J	ARG137

site_id	BC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE BR J 1104

Chain	Residue
J	TYR618

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG J 1105

Chain	Residue
J	ASP543
J	ASP552
R	U-1
R	U-2

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN J 1106

Chain	Residue
J	CYS47
J	CYS52
J	CYS55
J	HIS184

Functional Information from PROSITE/UniProt

site_id	PS01175
Number of Residues	25
Details	RIBONUCLEASE_II Ribonuclease II family signature. HYGLavdi.YThFTSPIRRYcDvvaH

Chain	Residue	Details
J	HIS831-HIS855

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	150
Details	Domain: {"description":"S1 motif"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	1
Details	Modified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	67
Details	Domain: {"description":"CSD2","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	330
Details	Domain: {"description":"RNB","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	97
Details	Domain: {"description":"S1 motif","evidences":[{"source":"PROSITE-ProRule","id":"PRU00180","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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