1P27

Crystal Structure of the Human Y14/Magoh 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	d1p27a_	Alpha and beta proteins (a+b)	Mago nashi protein	Mago nashi protein	Mago nashi protein	Mago nashi protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1p27c_	Alpha and beta proteins (a+b)	Mago nashi protein	Mago nashi protein	Mago nashi protein	Mago nashi protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1p27b_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	RNA-binding protein 8	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1p27d_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	RNA-binding protein 8	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	SCOP2B Superfamily	Mago nashi protein	8042952	3000634	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Mago nashi protein	8042952	3000634	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RNA-binding domain, RBD	8042953	3000110	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RNA-binding domain, RBD	8042953	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	Mago_nashi	e1p27A1	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_nashi	e1p27C1	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)
B	RRM_1_6	e1p27B1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)
D	RRM_1_6	e1p27D1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_6	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1560.10	Alpha Beta	2-Layer Sandwich	Mago nashi protein	Mago nashi	CATH (4.3.0)
C	3.30.1560.10	Alpha Beta	2-Layer Sandwich	Mago nashi protein	Mago nashi	CATH (4.3.0)
B	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
D	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	PF02792	Mago nashi protein (Mago_nashi)	Mago nashi protein	-	Family
B, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Mago nashi protein homolog	RNA binding binding organic cyclic compound binding nucleic acid binding	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing macromolecule metabolic 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 cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport intracellular transport establishment of localization RNA export from nucleus establishment of RNA localization macromolecule localization regulation of cellular process catabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process macromolecule catabolic process regulation of primary metabolic process regulation of RNA metabolic process regulation of mRNA catabolic process negative regulation of cellular process regulation of nucleobase-containing compound metabolic process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process regulation of biological process nuclear-transcribed mRNA catabolic process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process regulation of catabolic process regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of mRNA metabolic process regulation of metabolic process alternative mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA processing regulation of RNA splicing regulation of alternative mRNA splicing, via spliceosome regulation of protein metabolic process translation post-transcriptional regulation of gene expression regulation of translation protein metabolic process	membrane-bounded organelle exon-exon junction subcomplex mago-y14 protein-containing complex intracellular anatomical structure nucleus exon-exon junction complex nuclear protein-containing complex ATPase inhibitor complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle membrane-enclosed lumen intracellular organelle lumen membrane-bounded organelle exon-exon junction subcomplex mago-y14 protein-containing complex intracellular anatomical structure nucleus exon-exon junction complex nuclear protein-containing complex ATPase inhibitor complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle membrane-enclosed lumen intracellular organelle lumen nuclear speck nuclear body nucleoplasm organelle lumen nuclear lumen catalytic step 2 spliceosome catalytic complex spliceosomal complex ribonucleoprotein complex cytoplasm cytosol
B, D	RNA-binding protein 8A	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding	cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport intracellular transport gene expression establishment of localization macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process macromolecule localization cellular process metabolic process macromolecule metabolic process regulation of cellular process alternative mRNA splicing, via spliceosome RNA metabolic process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process nucleobase-containing compound 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 primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process regulation of RNA splicing mRNA metabolic process nucleic acid metabolic process regulation of gene expression 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 regulation of protein metabolic process translation post-transcriptional regulation of gene expression regulation of translation protein metabolic process catabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process mRNA catabolic process nuclear-transcribed mRNA catabolic process negative regulation of metabolic process regulation of catabolic process regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process	membrane-bounded organelle exon-exon junction subcomplex mago-y14 protein-containing complex intracellular anatomical structure nucleus exon-exon junction complex nuclear protein-containing complex ATPase inhibitor complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle membrane-enclosed lumen intracellular organelle lumen membrane-bounded organelle exon-exon junction subcomplex mago-y14 protein-containing complex intracellular anatomical structure nucleus exon-exon junction complex nuclear protein-containing complex ATPase inhibitor complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle membrane-enclosed lumen intracellular organelle lumen nuclear speck nuclear body nucleoplasm organelle lumen nuclear lumen U2-type spliceosomal complex catalytic complex U2-type catalytic step 1 spliceosome spliceosomal complex ribonucleoprotein complex catalytic step 1 spliceosome catalytic step 2 spliceosome cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection cell body neuronal cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR004023	Mago nashi protein	Family
A, C	IPR036605	Mago nashi superfamily	Homologous Superfamily
B, D	IPR033744	RBM8, RNA recognition motif	Domain
B, D	IPR000504	RNA recognition motif domain	Domain
B, D	IPR008111	RNA-binding motif protein 8	Family
B, D	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
B, D	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P61326	lymphoplasmacytic lymphoma plasma cell myeloma medulloblastoma ovarian cancer
B, D	Pharos: Q9Y5S9	thrombocytopenia-absent radius syndrome astrocytic tumor Cytopenia interstitial cystitis malignant mesothelioma ovarian cancer psoriasis tuberculosis breast cancer glioblastoma large cell medulloblastoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia congenital anemia intellectual disability thrombocytopenia-absent radius syndrome astrocytic tumor Cytopenia interstitial cystitis malignant mesothelioma ovarian cancer psoriasis tuberculosis breast cancer glioblastoma large cell medulloblastoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia congenital anemia intellectual disability lung cancer myopathy primitive neuroectodermal tumor

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.