1RK8
Structure of the cytosolic protein PYM bound to the Mago-Y14 core of the exon junction complex
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d1rk8a_ | Alpha and beta proteins (a+b) | Ferredoxin-like | RNA-binding domain, RBD, aka RNA recognition motif (RRM) | Canonical RBD | RNA-binding protein 8 | fruit fly (Drosophila melanogaster ) [TaxId: 7227 ], | SCOPe (2.08) |
B | d1rk8b_ | Alpha and beta proteins (a+b) | Mago nashi protein | Mago nashi protein | Mago nashi protein | Mago nashi protein | fruit fly (Drosophila melanogaster ) [TaxId: 7227 ], | SCOPe (2.08) |
C | d1rk8c_ | All beta proteins | WW domain-like | Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain | Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain | Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain | fruit fly (Drosophila melanogaster ) [TaxId: 7227 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | RNA-binding domain, RBD | 8034175 | 3000110 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Mago nashi protein | 8034173 | 3000634 | SCOP2B (2022-06-29) |
C | SCOP2 Family | Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain | 8028353 | 4000941 | SCOP2 (2022-06-29) |
C | SCOP2 Superfamily | Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain | 8040732 | 3000205 | SCOP2 (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_4 | e1rk8A1 | A: a+b two layers | X: Alpha-beta plaits | H: RNA-binding domain, RBD (From Topology) | T: RNA-binding domain, RBD | F: RRM_1_4 | ECOD (1.6) |
B | Mago_nashi | e1rk8B1 | A: a+b two layers | X: Mago nashi protein (From Topology) | H: Mago nashi protein (From Topology) | T: Mago nashi protein | F: Mago_nashi | ECOD (1.6) |
C | Mago-bind | e1rk8C1 | A: beta meanders | X: WW domain-like | H: Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain (From Topology) | T: Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain | F: Mago-bind | 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) |
B | 3.30.1560.10 | Alpha Beta | 2-Layer Sandwich | Mago nashi protein | Mago nashi | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
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 ... | Domain | |
PF02792 | Mago nashi protein (Mago_nashi) | Mago nashi protein | - | Family | |
PF09282 | Mago binding (Mago-bind) | Mago binding | Members of this family adopt a structure consisting of a small globular all-beta-domain, with a three-stranded beta-sheet and a contiguous beta-hairpin. They bind to Mago alpha-helices via extensive electrostatic interactions and at a beta2-beta3 loo ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR000504 | RNA recognition motif domain | Domain | |
IPR008111 | RNA-binding motif protein 8 | Family | |
IPR033744 | RBM8, RNA recognition motif | Domain | |
IPR012677 | Nucleotide-binding alpha-beta plait domain superfamily | Homologous Superfamily | |
IPR035979 | RNA-binding domain superfamily | Homologous Superfamily | |
IPR004023 | Mago nashi protein | Family | |
IPR036605 | Mago nashi superfamily | Homologous Superfamily | |
IPR036348 | WIBG, N-terminal domain superfamily | Homologous Superfamily | |
IPR039333 | Partner of Y14 and mago | Family | |
IPR015362 | WIBG, Mago-binding | Domain |