7S7C | pdb_00007s7c

Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	RNA-binding domain, RBD	8061925	3000110	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	RRM_1_1	e7s7cC1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_1	ECOD (1.6)
F [auth E]	rRNA_proc-arch_2nd	e7s7cE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: rRNA_proc-arch_2nd	ECOD (1.6)
F [auth E]	rRNA_proc-arch_3rd	e7s7cE2	A: extended segments	X: Helical arch in Ski2-like helicases (From Topology)	H: Helical arch in Ski2-like helicases (From Topology)	T: Helical arch in Ski2-like helicases	F: rRNA_proc-arch_3rd	ECOD (1.6)
A	rRNA_proc-arch_2nd	e7s7cA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: rRNA_proc-arch_2nd	ECOD (1.6)
A	KOG0948	e7s7cA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: KOG0948	ECOD (1.6)
A	DSHCT	e7s7cA5	A: alpha arrays	X: Sec63 N-terminal subdomain-like (From Topology)	H: Sec63 N-terminal subdomain-like (From Topology)	T: Sec63 N-terminal subdomain-like	F: DSHCT	ECOD (1.6)
A	DEAD_1	e7s7cA4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
A	Helicase_C_5	e7s7cA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_5	ECOD (1.6)
A	rRNA_proc-arch_3rd	e7s7cA6	A: extended segments	X: Helical arch in Ski2-like helicases (From Topology)	H: Helical arch in Ski2-like helicases (From Topology)	T: Helical arch in Ski2-like helicases	F: rRNA_proc-arch_3rd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00076	RNA recognition motif (RRM_1)	RNA recognition motif	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.	Domain
B, G [auth F]	PF04046	PSP (PSP)	PSP	-	Family
A, F [auth E]	PF08148	DSHCT (NUC185) domain (DSHCT)	DSHCT (NUC185) domain	This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [1].	Domain
A, F [auth E]	PF00270	DEAD/DEAH box helicase (DEAD)	DEAD/DEAH box helicase	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.	Domain
A, F [auth E]	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
A, F [auth E]	PF21408	Exosome RNA helicase MTR4-like, stalk (MTR4-like_stalk)	Exosome RNA helicase MTR4-like, stalk	Exosome RNA helicase MTR4 is a conserved RNA helicase that functions together with the nuclear exosome and it is involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclear RNA surveillance pathways involv ...	Exosome RNA helicase MTR4 is a conserved RNA helicase that functions together with the nuclear exosome and it is involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclear RNA surveillance pathways involving the so-called TRAMP complex [1,2]. It contains an arch domain, required for proper 5.8S rRNA processing, and appears to function independently of canonical helicase activity [3]. The arch domain comprises an helical stalk/elbow that flanks a KOW module which adopts a beta-barrel fold. This entry represents the helical stalk found at the N-terminal of KOW beta-barrel from MTR4 [1-3]. This entry also includes Ski2-like helicases which have an overall similar structure to MTR4 proteins. However, Ski2 from yeast does not have the KOW motif and the beta-barrel is tightly packed against the helical stalk [3].	Domain
A, F [auth E]	PF13234	Mtr4-like, beta-barrel domain (MTR4_beta-barrel)	Mtr4-like, beta-barrel domain	Exosome RNA helicase Mtr4 is a essential RNA helicase, and is an exosome-activating cofactor. It functions together with the nuclear exosome being involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclea ...	Exosome RNA helicase Mtr4 is a essential RNA helicase, and is an exosome-activating cofactor. It functions together with the nuclear exosome being involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclear RNA surveillance pathways involving the so-called TRAMP complex [1,2,3]. It contains an arch domain, required for proper 5.8S rRNA processing, and appears to function independently of canonical helicase activity [3]. The arch domain comprises an helical stalk/elbow that flanks a KOW module which adopts a beta-barrel fold. This entry represents the beta-barrel of MTR4 and related Ski2-like helicases. Ski2 from yeast has an overall similar structure to MTR4 proteins. However, it does not have the KOW motif [4] and it is not included in this entry.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E [auth L]	RNA (30-MER)	-	-	-
C	RNA-binding protein 7	protein binding binding 14-3-3 protein binding RNA binding snRNA binding nucleic acid binding single-stranded RNA binding pre-mRNA binding pre-mRNA intronic binding	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process snRNA metabolic process snRNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process snRNA metabolic process snRNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process regulation of cellular process alternative mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA metabolic process RNA processing regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of mRNA processing RNA splicing regulation of biological process biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of RNA splicing mRNA metabolic process macromolecule biosynthetic process regulation of gene expression biosynthetic process RNA splicing, via transesterification reactions regulation of alternative mRNA splicing, via spliceosome mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of macromolecule biosynthetic process regulation of mRNA metabolic process regulation of metabolic process sexual reproduction reproductive process meiotic cell cycle cell cycle	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen
B, G [auth F]	Zinc finger CCHC domain-containing protein 8	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding	mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process RNA splicing RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process snRNA metabolic process snRNA catabolic process nucleic acid catabolic process RNA catabolic process lncRNA processing co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway	membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex TRAMP complex membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex TRAMP complex membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear body nucleoplasm organelle lumen membraneless organelle nuclear lumen
A, F [auth E]	Exosome RNA helicase MTR4	RNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding RNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process RNA splicing mRNA processing mRNA metabolic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile snRNA metabolic process snRNA catabolic process maturation of 5.8S rRNA	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule catalytic step 2 spliceosome protein-containing complex catalytic complex nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex TRAMP complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR052285	Nuclear exosome targeting complex subunit	Family
C	IPR000504	RNA recognition motif domain	Domain
C	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
C	IPR034500	RBM7, RNA recognition motif	Domain
C	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
B, G [auth F]	IPR006568	PSP, proline-rich	Domain
B, G [auth F]	IPR001878	Zinc finger, CCHC-type	Domain
B, G [auth F]	IPR052115	Nuclear exosome targeting complex subunit ZCCHC8	Family
A, F [auth E]	IPR048392	Exosome RNA helicase MTR4-like, stalk	Domain
A, F [auth E]	IPR050699	RNA/DNA Helicase	Family
A, F [auth E]	IPR012961	ATP-dependent RNA helicase Ski2/MTR4, C-terminal	Domain
A, F [auth E]	IPR025696	Exosome RNA helicase MTR4-like, beta-barrel domain	Domain
A, F [auth E]	IPR011545	DEAD/DEAH-box helicase domain	Domain
A, F [auth E]	IPR016438	ATP-dependent RNA helicase SKI2-like	Family
A, F [auth E]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, F [auth E]	IPR001650	Helicase, C-terminal domain-like	Domain
A, F [auth E]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: Q9Y580	non-small cell lung carcinoma glioblastoma malignant ependymoma osteosarcoma medulloblastoma ovarian cancer
B, G [auth F]	Pharos: Q6NZY4	intellectual disability astrocytic tumor Mental deficiency ovarian cancer atypical teratoid rhabdoid tumor malignant mesothelioma plasma cell myeloma glioblastoma medulloblastoma osteosarcoma
A, F [auth E]	Pharos: P42285	ovarian cancer

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.