3NBY

Crystal structure of the PKI NES-CRM1-RanGTP nuclear export 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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	3002022	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	3002022	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8102757	3000798	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8102757	3000798	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)
B [auth C]	Ras	e3nbyC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
E [auth F]	Ras	e3nbyF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
A [auth B]	KOG3132	e3nbyB1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: KOG3132	ECOD (1.6)
A [auth B]	Snurportin1	e3nbyB2	A: extended segments	X: IBB domain (From Topology)	H: IBB domain (From Topology)	T: IBB domain	F: Snurportin1	ECOD (1.6)
D [auth E]	KOG3132	e3nbyE1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: KOG3132	ECOD (1.6)
D [auth E]	Snurportin1	e3nbyE2	A: extended segments	X: IBB domain (From Topology)	H: IBB domain (From Topology)	T: IBB domain	F: Snurportin1	ECOD (1.6)
C [auth A]	CRM1_C	e3nbyA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: CRM1_C	ECOD (1.6)
F [auth D]	CRM1_C	e3nbyD1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: CRM1_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E [auth F]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A [auth B]	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
D [auth E]	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], E [auth F]	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motil ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain
A [auth B], D [auth E]	PF11538	Snurportin1 (Snurportin1)	Snurportin1	-	Family
A [auth B], D [auth E]	PF21974	Snurportin1, m3G cap-binding domain (SPN1_m3Gcap_bd)	Snurportin1, m3G cap-binding domain	This entry represents the m3G cap-binding domain of Snurportin1 (SPN1), a nuclear import adaptor for m3G-capped spliceosomal U small nucleoproteins (snRNPs). After capping and assembly, the U snRNPs are transported into the nucleus by SPN1 and import ...	This entry represents the m3G cap-binding domain of Snurportin1 (SPN1), a nuclear import adaptor for m3G-capped spliceosomal U small nucleoproteins (snRNPs). After capping and assembly, the U snRNPs are transported into the nucleus by SPN1 and importin beta; SPN1 is then returned to the cytoplasm by exportin 1 (CRM1) [1-5].	Domain
C [auth A], F [auth D]	PF08389	Exportin 1-like protein (Xpo1)	Exportin 1-like protein	-	Repeat
C [auth A], F [auth D]	PF18784	CRM1 / Exportin repeat 2 (CRM1_repeat_2)	CRM1 / Exportin repeat 2	-	Repeat
C [auth A], F [auth D]	PF18777	Chromosome region maintenance or exportin repeat (CRM1_repeat)	Chromosome region maintenance or exportin repeat	-	Repeat
C [auth A], F [auth D]	PF18787	CRM1 / Exportin repeat 3 (CRM1_repeat_3)	CRM1 / Exportin repeat 3	-	Repeat
C [auth A], F [auth D]	PF03810	Importin-beta N-terminal domain (IBN_N)	Importin-beta N-terminal domain	-	Repeat
C [auth A], F [auth D]	PF08767	CRM1 C terminal (CRM1_C)	CRM1 C terminal	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C], E [auth F]	GTP-binding nuclear protein Ran	cell adhesion molecule binding cadherin binding protein binding binding dynein intermediate chain binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity protein domain specific binding chromatin binding cell adhesion molecule binding cadherin binding protein binding binding dynein intermediate chain binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity protein domain specific binding chromatin binding protein heterodimerization activity protein dimerization activity RNA binding organic cyclic compound binding nucleic acid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding magnesium ion binding metal ion binding GDP binding G protein activity molecular function regulator activity importin-alpha family protein binding	protein localization cellular localization establishment of protein localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport intracellular transport protein export from nucleus establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization protein localization cellular localization establishment of protein localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport intracellular transport protein export from nucleus establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process nuclear export intracellular protein transport viral process cell division protein localization to nucleus import into nucleus establishment of protein localization to organelle protein localization to organelle protein import into nucleus cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization regulation of localization regulation of cellular process regulation of protein localization positive regulation of nucleocytoplasmic transport positive regulation of biological process positive regulation of establishment of protein localization regulation of protein localization to nucleus positive regulation of protein transport regulation of protein import into nucleus positive regulation of intracellular transport positive regulation of cellular process regulation of intracellular transport regulation of biological process regulation of transport positive regulation of protein localization to nucleus biological regulation regulation of establishment of protein localization positive regulation of protein import into nucleus regulation of nucleocytoplasmic transport regulation of protein transport positive regulation of transport regulation of cellular localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation male gamete generation cell differentiation anatomical structure development germ cell development nucleobase-containing compound metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process GTP metabolic process carbohydrate derivative metabolic process nucleotide metabolic process purine-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process phosphorus metabolic process ribonucleoside triphosphate metabolic process regulation of protein binding positive regulation of molecular function regulation of molecular function positive regulation of protein binding regulation of binding positive regulation of binding cellular response to stimulus cellular response to mineralocorticoid stimulus response to lipid response to stimulus response to endogenous stimulus cellular response to organic cyclic compound response to mineralocorticoid cellular response to corticosteroid stimulus cellular response to endogenous stimulus response to corticosteroid cellular response to chemical stimulus response to hormone response to chemical response to steroid hormone cellular response to lipid cellular response to steroid hormone stimulus response to organic cyclic compound cellular response to hormone stimulus cell cycle mitotic cell cycle multicellular organismal process head development forebrain development animal organ development brain development nervous system development pallium development multicellular organism development central nervous system development telencephalon development hippocampus development limbic system development system development negative regulation of biological process post-transcriptional regulation of gene expression negative regulation of cellular process RNA localization nucleobase-containing compound transport negative regulation of macromolecule metabolic process regulation of biosynthetic process RNA transport negative regulation of metabolic process nucleic acid transport pre-miRNA export from nucleus regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing RNA export from nucleus regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing regulation of gene expression negative regulation of gene expression establishment of RNA localization biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing regulation of macromolecule biosynthetic process regulation of metabolic process establishment of organelle localization ribonucleoprotein complex biogenesis ribosomal subunit export from nucleus protein-containing complex localization cellular component biogenesis ribosome biogenesis ribosomal small subunit export from nucleus organelle localization ribosome localization ribosomal large subunit export from nucleus mitotic nuclear division organelle fission chromosome organization sister chromatid segregation nuclear division mitotic cell cycle process mitotic sister chromatid segregation nuclear chromosome segregation chromosome segregation cell cycle process protein localization to nucleolus microtubule cytoskeleton organization mitotic spindle organization microtubule-based process microtubule cytoskeleton organization involved in mitosis spindle organization RNA import into nucleus snRNA import into nucleus snRNA transport	cellular anatomical structure membrane protein-containing complex nucleocytoplasmic transport complex RNA nuclear export complex membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cellular anatomical structure membrane protein-containing complex nucleocytoplasmic transport complex RNA nuclear export complex membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol cell projection cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection nuclear protein-containing complex nuclear pore membraneless organelle intracellular membraneless organelle chromatin chromosome endosome intracellular vesicle recycling endosome cytoplasmic vesicle male germ cell nucleus germ cell nucleus midbody membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen pigment granule melanosome microtubule organizing center cytoskeleton centriole microtubule cytoskeleton nucleoplasm manchette
A [auth B], D [auth E]	Snurportin-1	nuclear import signal receptor activity nucleocytoplasmic carrier activity molecular carrier activity RNA binding binding organic cyclic compound binding nucleic acid binding RNA cap binding	cellular localization RNA import into nucleus RNA transport nitrogen compound transport nucleocytoplasmic transport transport nuclear transport nucleic acid transport intracellular transport establishment of localization localization import into nucleus establishment of RNA localization establishment of localization in cell macromolecule localization cellular localization RNA import into nucleus RNA transport nitrogen compound transport nucleocytoplasmic transport transport nuclear transport nucleic acid transport intracellular transport establishment of localization localization import into nucleus establishment of RNA localization establishment of localization in cell macromolecule localization cellular process RNA localization nucleobase-containing compound transport snRNA import into nucleus snRNA transport protein localization establishment of protein localization protein localization to nucleus establishment of protein localization to organelle protein transport cellular macromolecule localization protein localization to organelle protein import into nucleus intracellular protein transport	protein-containing complex nucleocytoplasmic transport complex NLS-dependent protein nuclear import complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle protein-containing complex nucleocytoplasmic transport complex NLS-dependent protein nuclear import complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope nuclear pore membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C [auth A], F [auth D]	Exportin-1	small GTPase binding protein binding binding enzyme binding GTPase binding protein domain specific binding RNA binding organic cyclic compound binding nucleic acid binding nucleocytoplasmic carrier activity nuclear export signal receptor activity molecular carrier activity transcription factor binding DNA-binding transcription factor binding	establishment of organelle localization cellular localization ribonucleoprotein complex biogenesis nucleocytoplasmic transport transport nuclear transport ribosomal subunit export from nucleus intracellular transport establishment of localization protein-containing complex localization cellular component biogenesis localization ribosome biogenesis ribosomal small subunit export from nucleus organelle localization establishment of organelle localization cellular localization ribonucleoprotein complex biogenesis nucleocytoplasmic transport transport nuclear transport ribosomal subunit export from nucleus intracellular transport establishment of localization protein-containing complex localization cellular component biogenesis localization ribosome biogenesis ribosomal small subunit export from nucleus organelle localization establishment of localization in cell cellular process cellular component organization or biogenesis nuclear export ribosome localization protein localization establishment of protein localization nitrogen compound transport protein export from nucleus protein transport cellular macromolecule localization macromolecule localization intracellular protein transport regulation of biological process regulation of cellular process catabolic process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process macromolecule catabolic process regulation of primary metabolic process metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process mRNA transport mRNA export from nucleus RNA localization nucleobase-containing compound transport RNA transport nucleic acid transport gene expression macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process microtubule organizing center organization regulation of cellular component organization regulation of centrosome cycle regulation of cell cycle process microtubule cytoskeleton organization regulation of microtubule-based process cellular component organization centrosome duplication organelle organization centrosome cycle regulation of centrosome duplication microtubule-based process cell cycle regulation of cell cycle cytoskeleton organization cell cycle process regulation of localization regulation of protein localization regulation of protein export from nucleus regulation of intracellular transport regulation of transport regulation of establishment of protein localization regulation of nucleocytoplasmic transport regulation of protein transport regulation of cellular localization regulation of intracellular protein transport ribosomal large subunit export from nucleus proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis modification-dependent macromolecule catabolic process proteolysis proteasomal protein catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process negative regulation of biological process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process protein localization to organelle protein localization to nucleus	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane cytoplasm cytosol chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome Cajal body nuclear body nucleoplasm protein-containing complex ribonucleoprotein complex nuclear outer membrane-endoplasmic reticulum membrane network annulate lamellae

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], E [auth F]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth C], E [auth F]	IPR002041	Ran GTPase	Family
B [auth C], E [auth F]	IPR005225	Small GTP-binding domain	Domain
B [auth C], E [auth F]	IPR001806	Small GTPase	Family
A [auth B], D [auth E]	IPR002652	Importin-alpha, importin-beta-binding domain	Domain
A [auth B], D [auth E]	IPR017336	Snurportin-1	Family
A [auth B], D [auth E]	IPR047857	Snurportin-1, m3G cap-binding domain	Domain
A [auth B], D [auth E]	IPR024721	Snurportin-1, N-terminal	Domain
C [auth A], F [auth D]	IPR041123	Chromosome region maintenance repeat	Repeat
C [auth A], F [auth D]	IPR016024	Armadillo-type fold	Homologous Superfamily
C [auth A], F [auth D]	IPR041235	Exportin-1, repeat 2	Repeat
C [auth A], F [auth D]	IPR001494	Importin-beta, N-terminal domain	Domain
C [auth A], F [auth D]	IPR011989	Armadillo-like helical	Homologous Superfamily
C [auth A], F [auth D]	IPR045065	Exportin-1/5	Family
C [auth A], F [auth D]	IPR013598	Exportin-1/Importin-beta-like	Domain
C [auth A], F [auth D]	IPR014877	Exportin-1, C-terminal	Domain
C [auth A], F [auth D]	IPR040485	Exportin-1, repeat 3	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C], E [auth F]	Pharos: P62826	keloid carcinoma HIV infectious disease Mammary Neoplasms, Experimental sarcomatoid carcinoma pemphigus undifferentiated carcinoma acute myeloid leukemia mammary neoplasms, animal nasopharyngeal carcinoma plasma cell myeloma amyotrophic lateral sclerosis lymphoplasmacytic lymphoma osteoarthritis ovarian cancer keloid carcinoma HIV infectious disease Mammary Neoplasms, Experimental sarcomatoid carcinoma pemphigus undifferentiated carcinoma acute myeloid leukemia mammary neoplasms, animal nasopharyngeal carcinoma plasma cell myeloma amyotrophic lateral sclerosis lymphoplasmacytic lymphoma osteoarthritis ovarian cancer invasive ductal breast carcinoma myopathy osteoarthritis susceptibility 1

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.