6D6Q

Human nuclear exosome-MTR4 RNA complex - overall reconstruction

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	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	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	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	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
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
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
I	0000176	cellular_component	nuclear 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
J	0000166	molecular_function	nucleotide binding
J	0000175	molecular_function	3'-5'-RNA exonuclease activity
J	0000176	cellular_component	nuclear 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	0006139	biological_process	nucleobase-containing compound metabolic process
J	0006396	biological_process	RNA processing
J	0008408	molecular_function	3'-5' exonuclease activity
K	0000175	molecular_function	3'-5'-RNA exonuclease activity
K	0000176	cellular_component	nuclear exosome (RNase complex)
K	0000177	cellular_component	cytoplasmic exosome (RNase complex)
K	0000178	cellular_component	exosome (RNase complex)
K	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
K	0000956	biological_process	nuclear-transcribed mRNA catabolic process
K	0003723	molecular_function	RNA binding
K	0004518	molecular_function	nuclease activity
K	0004519	molecular_function	endonuclease activity
K	0004527	molecular_function	exonuclease activity
K	0004540	molecular_function	RNA nuclease activity
K	0005085	molecular_function	guanyl-nucleotide exchange factor activity
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005730	cellular_component	nucleolus
K	0005737	cellular_component	cytoplasm
K	0005829	cellular_component	cytosol
K	0006364	biological_process	rRNA processing
K	0006396	biological_process	RNA processing
K	0006401	biological_process	RNA catabolic process
K	0016020	cellular_component	membrane
K	0016075	biological_process	rRNA catabolic process
K	0016787	molecular_function	hydrolase activity
K	0071031	biological_process	nuclear mRNA surveillance of mRNA 3'-end processing
K	0071034	biological_process	CUT catabolic process
L	0000176	cellular_component	nuclear exosome (RNase complex)
L	0000178	cellular_component	exosome (RNase complex)
L	0000460	biological_process	maturation of 5.8S rRNA
L	0003723	molecular_function	RNA binding
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005730	cellular_component	nucleolus
L	0005737	cellular_component	cytoplasm
L	0006364	biological_process	rRNA processing
M	0000166	molecular_function	nucleotide binding
M	0000176	cellular_component	nuclear exosome (RNase complex)
M	0000178	cellular_component	exosome (RNase complex)
M	0000398	biological_process	mRNA splicing, via spliceosome
M	0000460	biological_process	maturation of 5.8S rRNA
M	0003676	molecular_function	nucleic acid binding
M	0003723	molecular_function	RNA binding
M	0003724	molecular_function	RNA helicase activity
M	0004386	molecular_function	helicase activity
M	0005515	molecular_function	protein binding
M	0005524	molecular_function	ATP binding
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0005681	cellular_component	spliceosomal complex
M	0005730	cellular_component	nucleolus
M	0006364	biological_process	rRNA processing
M	0006397	biological_process	mRNA processing
M	0006401	biological_process	RNA catabolic process
M	0006974	biological_process	DNA damage response
M	0008380	biological_process	RNA splicing
M	0016076	biological_process	snRNA catabolic process
M	0016607	cellular_component	nuclear speck
M	0016787	molecular_function	hydrolase activity
M	0016887	molecular_function	ATP hydrolysis activity
M	0031499	cellular_component	TRAMP complex
M	0071013	cellular_component	catalytic step 2 spliceosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	binding site for residue MG K 2001

Chain	Residue
K	VAL478
O	A61

---

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN K 2002

Chain	Residue
K	CYS31
K	CYS36
K	CYS39
K	HIS159

---

site_id	AC3
Number of Residues	6
Details	binding site for residue ANP M 2001

Chain	Residue
M	THR168
M	ASN490
M	ARG527
M	PHE138
M	GLY166
M	LYS167

---

Functional Information from PROSITE/UniProt

site_id	PS01175
Number of Residues	25
Details	RIBONUCLEASE_II Ribonuclease II family signature. HYGLaspi.YThFTSPIRRYaDvivH

Chain	Residue	Details
K	HIS764-HIS788

---

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	3
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	4
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_FI5
Number of Residues	161
Details	Domain: {"description":"S1 motif"}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
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

---

site_id	SWS_FT_FI8
Number of Residues	118
Details	Domain: {"description":"PINc"}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	66
Details	Domain: {"description":"CSD2","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	Modified residue: {"description":"N-acetylmethionine","evidences":[{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	156
Details	Domain: {"description":"Helicase ATP-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	172
Details	Domain: {"description":"Helicase C-terminal","evidences":[{"source":"PROSITE-ProRule","id":"PRU00542","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	3
Details	Motif: {"description":"DEIH box"}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"31358741","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6RO1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29844170","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31358741","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6C90","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6RO1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---