Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4OO1

Structure of an Rrp6-RNA exosome complex bound to poly(A) 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	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
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	0000956	biological_process	nuclear-transcribed mRNA catabolic process
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	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	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
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	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	0000956	biological_process	nuclear-transcribed mRNA catabolic process
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	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
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	0000956	biological_process	nuclear-transcribed mRNA catabolic process
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	0000956	biological_process	nuclear-transcribed mRNA catabolic process
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	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
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	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
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	0000166	molecular_function	nucleotide binding
J	0000175	molecular_function	3'-5'-RNA exonuclease activity
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	0006139	biological_process	nucleobase-containing compound metabolic process
J	0008408	molecular_function	3'-5' exonuclease activity
J	0044237	biological_process	cellular metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG E 301

Chain	Residue
E	ASP81
E	ILE82
E	GLN85
E	ASP87

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MPD E 302

Chain	Residue
E	SER9
E	ASN235

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MES G 301

Chain	Residue
A	LYS13
G	GLY153
G	CYS198

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PO4 I 301

Chain	Residue
I	ARG150
S	PO4102

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG S 101

Chain	Residue
J	ASN238
S	A23
S	A24

site_id	AC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PO4 S 102

Chain	Residue
I	PO4301

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:16882719, ECO:0007744\|PDB:2HBL, ECO:0007744\|PDB:2HBM

Chain	Residue	Details
J	ASN238
J	GLU240
J	ASP365

site_id	SWS_FT_FI2
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:16882719, ECO:0007744\|PDB:2HBM

Chain	Residue	Details
J	HIS241
J	TRP299
J	LYS342
J	GLN345

site_id	SWS_FT_FI3
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:16882719, ECO:0007744\|PDB:2HBK, ECO:0007744\|PDB:2HBL, ECO:0007744\|PDB:2HBM

Chain	Residue	Details
J	ASP296

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17330950

Chain	Residue	Details
J	SER138

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:18407956

Chain	Residue	Details
J	THR520

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:19779198

Chain	Residue	Details
J	SER640

site_id	SWS_FT_FI7
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17330950, ECO:0007744\|PubMed:18407956, ECO:0007744\|PubMed:19779198

Chain	Residue	Details
J	SER645

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