1RK8

Structure of the cytosolic protein PYM bound to the Mago-Y14 core of the exon junction 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

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	PF00076	e1rk8A1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: PF00076	ECOD (1.6)
B	PF02792	e1rk8B1	A: a+b two layers	X: Mago nashi protein (From Topology)	H: Mago nashi protein (From Topology)	T: Mago nashi protein	F: PF02792	ECOD (1.6)
C	PF09282	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: PF09282	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
A	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	PF02792	Mago nashi protein (Mago_nashi)	Mago nashi protein	-	Family
C	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 ...	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 loop via hydrophobic interactions [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CG8781-PA protein	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding	localization cellular localization import into nucleus nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport cellular process establishment of localization RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process localization cellular localization import into nucleus nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport cellular process establishment of localization RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process RNA processing macromolecule metabolic process oocyte dorsal/ventral axis specification multicellular organismal process sexual reproduction cellular developmental process reproductive process cell development cellular process involved in reproduction in multicellular organism pattern specification process developmental process involved in reproduction female gamete generation gamete generation oocyte development multicellular organism development oocyte nucleus localization involved in oocyte dorsal/ventral axis specification cell differentiation organelle localization anatomical structure development cell maturation developmental process oocyte axis specification oocyte construction multicellular organismal reproductive process oogenesis dorsal/ventral axis specification nucleus localization developmental maturation regionalization dorsal/ventral pattern formation anatomical structure maturation germ cell development oocyte differentiation axis specification RNA transport nitrogen compound transport organic substance transport nucleic acid transport mRNA transport establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport blastoderm segmentation anterior/posterior pattern specification anterior/posterior axis specification, embryo establishment of pole plasm mRNA localization cellular component biogenesis cellular component assembly cellular macromolecule localization pole plasm mRNA localization pole plasm RNA localization embryonic pattern specification oocyte anterior/posterior axis specification cytoplasm organization maternal determination of anterior/posterior axis, embryo intracellular mRNA localization involved in anterior/posterior axis specification segmentation embryo development tripartite regional subdivision cellular component organization embryonic axis specification anterior/posterior axis specification cellular component organization or biogenesis intracellular mRNA localization pole plasm assembly intracellular mRNA localization involved in pattern specification process mRNA processing mRNA metabolic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile organelle organization microtubule cytoskeleton organization microtubule-based process cytoskeleton organization cell fate determination germarium-derived oocyte fate determination oocyte fate determination germarium-derived egg chamber formation germarium-derived oocyte differentiation anatomical structure morphogenesis anatomical structure formation involved in morphogenesis cell fate commitment regulation of localization regulation of cellular process pole plasm oskar mRNA localization regulation of biological process regulation of intracellular mRNA localization regulation of pole plasm oskar mRNA localization biological regulation regulation of cellular localization	protein-containing complex nucleocytoplasmic transport complex NLS-dependent protein nuclear import complex membrane-bounded organelle catalytic step 2 spliceosome intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle spliceosomal complex organelle protein-containing complex nucleocytoplasmic transport complex NLS-dependent protein nuclear import complex membrane-bounded organelle catalytic step 2 spliceosome intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle spliceosomal complex organelle ribonucleoprotein complex exon-exon junction complex cytoplasm
B	Mago nashi protein	RNA binding binding organic cyclic compound binding nucleic acid binding	localization cellular localization import into nucleus nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport cellular process establishment of localization RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process localization cellular localization import into nucleus nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport cellular process establishment of localization RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process RNA processing macromolecule metabolic process developmental process sexual reproduction cellular developmental process reproductive process oogenesis multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism female gamete generation developmental process involved in reproduction gamete generation cell differentiation anatomical structure development germ cell development protein localization cellular macromolecule localization macromolecule localization RNA transport nitrogen compound transport organic substance transport nucleic acid transport mRNA transport establishment of RNA localization RNA localization nucleobase-containing compound transport mRNA processing mRNA metabolic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of cellular process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of cellular biosynthetic process cellular component organization organelle organization microtubule cytoskeleton organization microtubule-based process cellular component organization or biogenesis cytoskeleton organization multicellular organismal process blastoderm segmentation anterior/posterior pattern specification anterior/posterior axis specification, embryo segmentation pattern specification process embryo development oocyte development tripartite regional subdivision cellular component biogenesis embryonic axis specification multicellular organism development cellular component assembly anterior/posterior axis specification cell maturation embryonic pattern specification oocyte axis specification oocyte construction oocyte anterior/posterior axis specification developmental maturation cytoplasm organization regionalization pole plasm assembly anatomical structure maturation maternal determination of anterior/posterior axis, embryo oocyte differentiation axis specification maintenance of pole plasm mRNA location pole plasm mRNA localization maintenance of RNA location pole plasm RNA localization maintenance of location intracellular mRNA localization involved in anterior/posterior axis specification maintenance of location in cell intracellular mRNA localization intracellular mRNA localization involved in pattern specification process establishment or maintenance of cell polarity establishment or maintenance of microtubule cytoskeleton polarity establishment or maintenance of cytoskeleton polarity oocyte microtubule cytoskeleton organization oocyte microtubule cytoskeleton polarization regulation of localization pole plasm oskar mRNA localization regulation of intracellular mRNA localization regulation of pole plasm oskar mRNA localization regulation of cellular localization	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle spliceosomal complex organelle ribonucleoprotein complex precatalytic spliceosome nucleocytoplasmic transport complex NLS-dependent protein nuclear import complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle spliceosomal complex organelle ribonucleoprotein complex precatalytic spliceosome nucleocytoplasmic transport complex NLS-dependent protein nuclear import complex catalytic step 2 spliceosome catalytic complex exon-exon junction complex cytoplasm pole plasm
C	Within the bgcn gene intron protein	RNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding exon-exon junction complex binding	regulation of cellular process catabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of cellular process catabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process organic substance catabolic process cellular component organization cellular component disassembly protein-containing complex organization protein-containing complex disassembly cellular component organization or biogenesis exon-exon junction complex disassembly	membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus exon-exon junction complex nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000504	RNA recognition motif domain	Domain
A	IPR008111	RNA-binding motif protein 8	Family
A	IPR033744	RBM8, RNA recognition motif	Domain
A	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
B	IPR004023	Mago nashi protein	Family
B	IPR036605	Mago nashi superfamily	Homologous Superfamily
C	IPR036348	WIBG, N-terminal domain superfamily	Homologous Superfamily
C	IPR039333	Partner of Y14 and mago	Family
C	IPR015362	WIBG, Mago-binding	Domain

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 R01GM133198.