Annotations: 3IKO

Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Coat and nuclear envelope proteins	8054129	3002276	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Coat and nuclear envelope proteins	8054129	3002276	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Coat and nuclear envelope proteins	8054129	3002276	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	PDEase_I	e3ikoA1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: PDEase_I	ECOD (v295.2)
G	PDEase_I	e3ikoG1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: PDEase_I	ECOD (v295.2)
D	PDEase_I	e3ikoD1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: PDEase_I	ECOD (v295.2)
B	PDEase_I	e3ikoB1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: PDEase_I	ECOD (v295.2)
E	PDEase_I	e3ikoE1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: PDEase_I	ECOD (v295.2)
H	PDEase_I	e3ikoH1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: PDEase_I	ECOD (v295.2)
C	Nup84_Nup100	e3ikoC1	A: alpha arrays	X: Repetitive alpha hairpins	H: Nucleoporin Nup84/Nup107	T: Nucleoporin Nup84/Nup107	F: Nup84_Nup100	ECOD (v295.2)
F	PDEase_I	e3ikoF1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: PDEase_I	ECOD (v295.2)
I	PDEase_I	e3ikoI1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: PDEase_I	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
G	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
D	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B	1.25.40.690	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
E	6.20.50.170	Special	Other non-globular	N-terminal domain of TfIIb		CATH (4.3.0)
E	1.25.40.690	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
H	6.20.50.170	Special	Other non-globular	N-terminal domain of TfIIb		CATH (4.3.0)
H	1.25.40.690	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C	1.10.3450.20	Mainly Alpha	Orthogonal Bundle	Hyaluronidase domain-like		CATH (4.3.0)
F	1.10.3450.20	Mainly Alpha	Orthogonal Bundle	Hyaluronidase domain-like		CATH (4.3.0)
I	1.10.3450.20	Mainly Alpha	Orthogonal Bundle	Hyaluronidase domain-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
B, E, H	PF12110	Nucleoporin Nup96/Nup145C alpha-helical domain (Nup96)	Nucleoporin Nup96/Nup145C alpha-helical domain	-	Repeat
C, F, I	PF04121	Nuclear pore protein 84 / 107 (Nup84_Nup100)	Nuclear pore protein 84 / 107	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G	Protein transport protein SEC13	structural molecule activity	nuclear pore localization cellular localization localization within membrane protein-containing complex localization cellular component organization localization nucleus organization organelle organization macromolecule localization cellular process cellular component organization or biogenesis regulation of localization regulation of cellular process transport nuclear pore localization cellular localization localization within membrane protein-containing complex localization cellular component organization localization nucleus organization organelle organization macromolecule localization cellular process cellular component organization or biogenesis regulation of localization regulation of cellular process transport positive regulation of biological process positive regulation of ER to Golgi vesicle-mediated transport vesicle-mediated transport establishment of localization in cell positive regulation of intracellular transport positive regulation of cellular process regulation of intracellular transport regulation of biological process regulation of ER to Golgi vesicle-mediated transport regulation of transport biological regulation intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport regulation of vesicle-mediated transport establishment of localization positive regulation of transport regulation of cellular localization Golgi vesicle transport membrane organization vesicle budding from membrane vesicle organization COPII-coated vesicle budding cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress positive regulation of cell communication positive regulation of signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction TOR signaling regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of signaling nucleocytoplasmic transport nuclear transport regulation of TORC1 signaling TORC1 signaling establishment of protein localization protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport positive regulation of TORC1 signaling positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex nuclear pore outer ring intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex nuclear pore outer ring intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore cell periphery vesicle coat intracellular vesicle transport vesicle membrane membrane protein complex membrane coat bounding membrane of organelle vesicle membrane cytoplasmic vesicle ER to Golgi transport vesicle membrane coated vesicle vesicle transport vesicle membrane coated membrane COPII vesicle coat cytoplasmic vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle cytoplasm organelle membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane Seh1-associated complex endoplasmic reticulum exit site vacuolar membrane vacuole
B, E, H	Nucleoporin NUP145C	RNA binding binding nucleic acid binding structural molecule activity structural constituent of nuclear pore	nuclear pore localization cellular localization localization within membrane protein-containing complex localization cellular component organization localization nucleus organization organelle organization macromolecule localization cellular process cellular component organization or biogenesis telomere localization telomere tethering at nuclear periphery chromosome localization nuclear pore localization cellular localization localization within membrane protein-containing complex localization cellular component organization localization nucleus organization organelle organization macromolecule localization cellular process cellular component organization or biogenesis telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization RNA transport nitrogen compound transport nucleocytoplasmic transport transport nuclear transport nucleic acid transport intracellular transport tRNA export from nucleus establishment of localization RNA export from nucleus tRNA transport establishment of RNA localization establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport protein localization to nucleus protein localization to membrane protein localization to nuclear envelope protein localization to organelle intracellular protein localization protein localization to nuclear inner membrane regulation of localization regulation of biological process regulation of cellular process regulation of transport biological regulation regulation of nucleocytoplasmic transport regulation of cellular localization regulation of intracellular transport establishment of protein localization import into nucleus establishment of protein localization to organelle protein transport protein import into nucleus intracellular protein transport mRNA transport mRNA export from nucleus poly(A)+ mRNA export from nucleus gene expression macromolecule biosynthetic process biosynthetic process metabolic process macromolecule metabolic process NLS-bearing protein import into nucleus subtelomeric heterochromatin formation negative regulation of biological process cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization regulation of macromolecule metabolic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular response to stimulus double-strand break repair response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair chromosome organization transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex nuclear pore outer ring intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex nuclear pore outer ring intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore nuclear membrane membrane organelle membrane nuclear pore central transport channel membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region nuclear pore cytoplasmic filaments
C, F, I	Nucleoporin NUP84	structural molecule activity structural constituent of nuclear pore identical protein binding protein binding binding	nuclear pore localization cellular localization localization within membrane protein-containing complex localization cellular component organization localization nucleus organization organelle organization macromolecule localization cellular process cellular component organization or biogenesis telomere localization telomere tethering at nuclear periphery chromosome localization nuclear pore localization cellular localization localization within membrane protein-containing complex localization cellular component organization localization nucleus organization organelle organization macromolecule localization cellular process cellular component organization or biogenesis telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport 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 positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription silent mating-type cassette heterochromatin formation cellular response to stimulus double-strand break repair response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair chromosome organization transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery establishment of protein localization protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II response to heat response to temperature stimulus cellular response to heat response to nitrogen compound mRNA export from nucleus in response to heat stress response to chemical response to abiotic stimulus	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex nuclear pore outer ring intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex nuclear pore outer ring intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore nuclear membrane membrane organelle membrane membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, D, G	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, D, G	IPR037363	Sec13/Seh1 family	Family
A, D, G	IPR001680	WD40 repeat	Repeat
B, E, H	IPR025574	Nucleoporin FG repeat	Repeat
B, E, H	IPR037665	Nucleoporin peptidase S59-like	Family
B, E, H	IPR036903	Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily	Homologous Superfamily
B, E, H	IPR007230	Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain	Domain
B, E, H	IPR021967	Nuclear pore complex protein NUP96, C-terminal domain	Domain
C, F, I	IPR007252	Nuclear pore protein 84/107	Family