5LXY

Structure of the minimal RBM7 - ZCCHC8 Complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5lxya_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d5lxyb_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5lxye_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5lxyg_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d5lxyi_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d5lxyk_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
M	d5lxym_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Canonical RBD	8061924	4000236	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RNA-binding domain, RBD	8061925	3000110	SCOP2 (2022-06-29)
C [auth B]	SCOP2B Superfamily	RNA-binding domain, RBD	8061925	3000110	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RNA-binding domain, RBD	8061925	3000110	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RNA-binding domain, RBD	8061925	3000110	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	RNA-binding domain, RBD	8061925	3000110	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	RNA-binding domain, RBD	8061925	3000110	SCOP2B (2022-06-29)
M	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)
A	RRM_1_1	e5lxyA1	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)
C [auth B]	RRM_1_1	e5lxyB1	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)
E	RRM_1_1	e5lxyE1	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)
G	RRM_1_1	e5lxyG1	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)
I	RRM_1_1	e5lxyI1	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)
K	RRM_1_1	e5lxyK1	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)
M	RRM_1_1	e5lxyM1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
C [auth B]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
E	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
G	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
I	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
K	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
M	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E, G, I, A, C [auth B], E, G, I, K, M	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 [auth D], D [auth C], F, H, J, B [auth D], D [auth C], F, H, J, L, N	PF04046	PSP (PSP)	PSP	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B], E, G, I, A, C [auth B], E, G, I, K, M	RNA-binding protein 7	protein binding binding 14-3-3 protein binding RNA binding snRNA binding organic cyclic compound 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 macromolecule metabolic process RNA catabolic process regulation of cellular 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 macromolecule metabolic process RNA catabolic process regulation of cellular process alternative mRNA splicing, via spliceosome cellular biosynthetic process 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 cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of RNA splicing mRNA metabolic process macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process RNA splicing, via transesterification reactions regulation of alternative mRNA splicing, via spliceosome mRNA splicing, via spliceosome cellular process 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 cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
B [auth D], D [auth C], F, H, J, B [auth D], D [auth C], F, H, J, L, N	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 organic cyclic compound binding nucleic acid binding	cellular biosynthetic process mRNA 3'-end processing cellular metabolic process 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 cellular biosynthetic process mRNA 3'-end processing cellular metabolic process 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	membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle 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 cellular anatomical entity intracellular organelle spliceosomal complex organelle ribonucleoprotein complex TRAMP complex membrane-enclosed lumen intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E, G, I, A, C [auth B], E, G, I, K, M	IPR052285	Nuclear exosome targeting complex subunit	Family
A, C [auth B], E, G, I, A, C [auth B], E, G, I, K, M	IPR000504	RNA recognition motif domain	Domain
A, C [auth B], E, G, I, A, C [auth B], E, G, I, K, M	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, C [auth B], E, G, I, A, C [auth B], E, G, I, K, M	IPR034500	RBM7, RNA recognition motif	Domain
A, C [auth B], E, G, I, A, C [auth B], E, G, I, K, M	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
B [auth D], D [auth C], F, H, J, B [auth D], D [auth C], F, H, J, L, N	IPR006568	PSP, proline-rich	Domain
B [auth D], D [auth C], F, H, J, B [auth D], D [auth C], F, H, J, L, N	IPR001878	Zinc finger, CCHC-type	Domain
B [auth D], D [auth C], F, H, J, B [auth D], D [auth C], F, H, J, L, N	IPR052115	Nuclear exosome targeting complex subunit ZCCHC8	Family

Pharos: Disease Associations Pharos Homepage Annotation

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

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.