3FEX | pdb_00003fex

Crystal structure of the CBC-importin alpha 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)
C	SCOP2B Superfamily	ARM repeat-like	8081893	3000116	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RNA-binding domain, RBD	8042382	3000110	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8042371	3000116	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8042373	3000116	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ARM repeat-like	8042374	3000116	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)
C	Arm	e3fexC1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Arm	ECOD (1.6)
B	RRM_1_6	e3fexB1	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)
A	MIF4G	e3fexA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: MIF4G	ECOD (1.6)
A	MIF4G_like	e3fexA2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: MIF4G_like	ECOD (1.6)
A	MIF4G_like_2	e3fexA3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: MIF4G_like_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	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)
A	1.25.40.180	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00514	Armadillo/beta-catenin-like repeat (Arm)	Armadillo/beta-catenin-like repeat	-	Repeat
C	PF01749	Importin beta binding domain (IBB)	Importin beta binding domain	-	Repeat
C	PF16186	Atypical Arm repeat (Arm_3)	Atypical Arm repeat	-	Repeat
B	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
A	PF09088	MIF4G like (MIF4G_like)	MIF4G like	-	Repeat
A	PF09090	MIF4G like (MIF4G_like_2)	MIF4G like	-	Repeat
A	PF02854	MIF4G domain (MIF4G)	MIF4G domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Importin subunit alpha-2	histone deacetylase binding protein binding binding enzyme binding RNA binding nucleic acid binding nuclear localization sequence binding signal sequence binding peptide binding nuclear import signal receptor activity nucleocytoplasmic carrier activity molecular carrier activity	regulation of DNA recombination regulation of biological process regulation of cellular process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process metabolic process cellular process macromolecule metabolic process regulation of DNA recombination regulation of biological process regulation of cellular process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process metabolic process cellular process macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA metabolic process establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport regulation of viral process regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral process viral process positive regulation of biological process viral life cycle NLS-bearing protein import into nucleus multicellular organismal process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of multicellular organismal process positive regulation of cellular process regulation of biosynthetic process positive regulation of type I interferon production type I interferon production gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of type I interferon production biological process involved in interspecies interaction between organisms viral penetration into host nucleus entry of viral genome into host nucleus through nuclear pore complex via importin intracellular transport of virus transport of virus biological process involved in symbiotic interaction	protein-containing complex nucleocytoplasmic transport complex NLS-dependent protein nuclear import complex cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle protein-containing complex nucleocytoplasmic transport complex NLS-dependent protein nuclear import complex cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane host cellular component host cell other organism part Golgi membrane Golgi apparatus bounding membrane of organelle
B	Nuclear cap-binding protein subunit 2	RNA binding binding nucleic acid binding RNA cap binding DNA binding snRNA binding mRNA binding RNA 7-methylguanosine cap binding	regulation of cellular process positive regulation of biological process RNA metabolic process mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process RNA 3'-end processing regulation of nucleobase-containing compound metabolic process RNA processing regulation of cellular process positive regulation of biological process RNA metabolic process mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process RNA 3'-end processing regulation of nucleobase-containing compound metabolic process RNA processing positive regulation of cellular process regulation of mRNA processing regulation of biological process positive regulation of nucleobase-containing compound metabolic process mRNA 3'-end processing biological regulation regulation of mRNA 3'-end processing positive regulation of mRNA metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process biosynthetic process positive regulation of mRNA processing metabolic process cellular process macromolecule metabolic process positive regulation of mRNA 3'-end processing regulation of mRNA metabolic process regulation of metabolic process RNA splicing RNA splicing, via transesterification reactions mRNA cis splicing, via spliceosome mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of nucleobase-containing compound transport localization positive regulation of RNA export from nucleus establishment of localization in cell positive regulation of intracellular transport RNA localization nuclear export nucleobase-containing compound transport regulation of intracellular transport RNA transport regulation of transport regulation of nucleobase-containing compound transport regulation of RNA export from nucleus nucleic acid transport intracellular transport regulation of nucleocytoplasmic transport establishment of localization RNA export from nucleus establishment of RNA localization positive regulation of transport regulation of cellular localization macromolecule localization negative regulation of biological process post-transcriptional regulation of gene expression negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing regulation of macromolecule biosynthetic process mRNA transport mRNA export from nucleus cap-dependent translational initiation translation cytoplasmic translation cytoplasmic translational initiation translational initiation protein metabolic process histone mRNA metabolic process regulation of translational initiation regulation of protein metabolic process regulation of translation mRNA transcription by RNA polymerase II mRNA transcription DNA-templated transcription transcription by RNA polymerase II regulatory ncRNA processing primary miRNA processing miRNA processing transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of DNA-templated transcription catabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay macromolecule catabolic process RNA catabolic process mRNA catabolic process nuclear-transcribed mRNA catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process miRNA-mediated post-transcriptional gene silencing alternative mRNA splicing, via spliceosome snRNA export from nucleus snRNA transport	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex RNA cap binding complex intracellular protein-containing complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex RNA cap binding complex intracellular protein-containing complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen nuclear cap binding complex intracellular membraneless organelle cilium plasma membrane bounded cell projection ciliary basal body cell projection microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton
A	Nuclear cap-binding protein subunit 1	RNA binding binding nucleic acid binding RNA cap binding mRNA binding RNA 7-methylguanosine cap binding molecular adaptor activity	regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process RNA metabolic process mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process RNA 3'-end processing regulation of nucleobase-containing compound metabolic process RNA processing regulation of mRNA processing positive regulation of nucleobase-containing compound metabolic process mRNA 3'-end processing regulation of mRNA 3'-end processing positive regulation of mRNA metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process biosynthetic process positive regulation of mRNA processing metabolic process macromolecule metabolic process positive regulation of mRNA 3'-end processing regulation of mRNA metabolic process regulation of metabolic process negative regulation of biological process post-transcriptional regulation of gene expression negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing regulation of macromolecule biosynthetic process 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 cap-dependent translational initiation translation cytoplasmic translation cytoplasmic translational initiation translational initiation protein metabolic process positive regulation of molecular function regulation of molecular function positive regulation of RNA binding regulation of binding positive regulation of binding catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process RNA splicing ribonucleoprotein complex biogenesis protein-RNA complex assembly cellular component biogenesis spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly protein-containing complex organization RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile histone mRNA metabolic process regulation of translational initiation regulation of protein metabolic process regulation of translation mRNA transcription by RNA polymerase II mRNA transcription DNA-templated transcription transcription by RNA polymerase II regulatory ncRNA processing primary miRNA processing miRNA processing transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of DNA-templated transcription 7-methylguanosine mRNA capping 7-methylguanosine RNA capping RNA capping RNA 5'-end processing nuclear-transcribed mRNA catabolic process, nonsense-mediated decay mRNA catabolic process nuclear-transcribed mRNA catabolic process biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus miRNA-mediated post-transcriptional gene silencing alternative mRNA splicing, via spliceosome snRNA export from nucleus snRNA transport regulation of mRNA splicing, via spliceosome positive regulation of mRNA splicing, via spliceosome regulation of RNA splicing positive regulation of gene expression positive regulation of RNA splicing	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol protein-containing complex RNA cap binding complex intracellular protein-containing complex nucleus membrane-enclosed lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol protein-containing complex RNA cap binding complex intracellular protein-containing complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nuclear cap binding complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR016024	Armadillo-type fold	Homologous Superfamily
C	IPR000225	Armadillo	Repeat
C	IPR011989	Armadillo-like helical	Homologous Superfamily
C	IPR024931	Importin subunit alpha	Family
C	IPR036975	Importin-alpha, importin-beta-binding domain superfamily	Homologous Superfamily
C	IPR002652	Importin-alpha, importin-beta-binding domain	Domain
C	IPR032413	Atypical Arm repeat	Repeat
B	IPR034148	NCBP2, RNA recognition motif	Domain
B	IPR000504	RNA recognition motif domain	Domain
B	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
B	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
B	IPR027157	Nuclear cap-binding protein subunit 2	Family
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR015172	MIF4G-like, type 1	Domain
A	IPR027159	Nuclear cap-binding protein subunit 1	Family
A	IPR015174	MIF4G-like, type 2	Domain
A	IPR003890	MIF4G-like, type 3	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: P52292	lung adenocarcinoma acute myeloid leukemia IgA glomerulonephritis peripheral arterial disease Adenocarcinoma of Lung psoriasis non-small cell lung carcinoma
B	Pharos: P52298	astrocytic tumor lung adenocarcinoma myopathy breast cancer lung cancer non-small cell lung carcinoma breast carcinoma medulloblastoma ovarian cancer
A	Pharos: Q09161	Barrett esophagus esophageal adenocarcinoma malignant ependymoma myopathy thyroid gland carcinoma breast cancer Hashimoto thyroiditis malignant mesothelioma non-small cell lung carcinoma tuberculosis breast carcinoma hypothyroidism medulloblastoma pancreatic intraductal papillary-mucinous carcinoma

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.