Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6D6R

Human nuclear exosome-MTR4 RNA complex - composite map after focused 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	0043231	cellular_component	intracellular membrane-bounded organelle
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	1902494	cellular_component	catalytic 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	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	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	0005694	cellular_component	chromosome
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	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	0043231	cellular_component	intracellular membrane-bounded organelle
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	1902494	cellular_component	catalytic 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	0000956	biological_process	nuclear-transcribed mRNA catabolic process
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	1902494	cellular_component	catalytic 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	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	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	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	1902494	cellular_component	catalytic 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	0000956	biological_process	nuclear-transcribed mRNA catabolic process
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	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	0045830	biological_process	positive regulation of 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)
F	1902494	cellular_component	catalytic 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	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	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	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	0034475	biological_process	U4 snRNA 3'-end processing
G	0045006	biological_process	DNA deamination
G	0045190	biological_process	isotype switching
G	0045830	biological_process	positive regulation of 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	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	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)
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
J	0044237	biological_process	cellular metabolic process
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	0003723	molecular_function	RNA binding
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	0008408	molecular_function	3'-5' exonuclease activity
K	0016020	cellular_component	membrane
K	0016075	biological_process	rRNA catabolic process
K	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
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	0005829	cellular_component	cytosol
L	0006364	biological_process	rRNA processing
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	4
Details	binding site for residue ZN K 1001

Chain	Residue
K	CYS31
K	CYS36
K	CYS39
K	HIS159

site_id	AC2
Number of Residues	3
Details	binding site for residue MG K 2001

Chain	Residue
K	VAL478
K	ASP488
O	A61

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

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

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	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:31358741, ECO:0007744\|PDB:6RO1

Chain	Residue	Details
M	ILE139
J	GLU315
J	ASP440

site_id	SWS_FT_FI2
Number of Residues	1
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00541

Chain	Residue	Details
M	ALA161

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:29844170, ECO:0000269\|PubMed:31358741, ECO:0007744\|PDB:6C90, ECO:0007744\|PDB:6RO1

Chain	Residue	Details
M	SER164
M	GLY166
M	LYS167
M	THR168

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: N-acetylalanine => ECO:0000269\|Ref.6, ECO:0007744\|PubMed:19413330, ECO:0007744\|PubMed:22223895

Chain	Residue	Details
M	ALA2
L	LYS153
J	LYS666

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
M	SER40
A	SER411

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
M	LYS51

site_id	SWS_FT_FI7
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:Q9CZU3

Chain	Residue	Details
M	LYS78
A	LYS436

site_id	SWS_FT_FI8
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744\|PubMed:28112733

Chain	Residue	Details
M	LYS24
M	LYS358
M	LYS723

site_id	SWS_FT_FI9
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744\|PubMed:25772364, ECO:0007744\|PubMed:28112733

Chain	Residue	Details
M	LYS684

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