3A6P | pdb_00003a6p

Crystal structure of Exportin-5:RanGTP:pre-miRNA 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)
H	d3a6ph_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Ran	dogs (Canis lupus familiaris ) [TaxId: 9615 ],	SCOPe (2.08)
C	d3a6pc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Ran	dogs (Canis lupus familiaris ) [TaxId: 9615 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Ras-like P-loop GTPases	8060226	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8060226	3002022	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)
H	adh_short	e3a6pH1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: adh_short	ECOD (develop294)
C	adh_short	e3a6pC1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: adh_short	ECOD (develop294)
F	Flavodoxin_2	e3a6pF1	A: alpha bundles	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: Flavodoxin_2	ECOD (develop294)
A	IspD	e3a6pA1	A: alpha bundles	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: IspD	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)
A	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, H	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, motili ...	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, F	PF19273	Exportin-5 family (Exportin-5)	Exportin-5 family	-	Repeat
A, F	PF08389	Exportin 1-like protein (Xpo1)	Exportin 1-like protein	-	Repeat
A, F	PF03810	Importin-beta N-terminal domain (IBN_N)	Importin-beta N-terminal domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, J	pre-microRNA	-	-	-
D, I	pre-microRNA	-	-	-
C, H	GTP-binding nuclear protein Ran	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 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 nucleocytoplasmic carrier activity nuclear export signal receptor activity molecular carrier activity cation binding magnesium ion binding metal ion binding RISC complex binding ribonucleoprotein complex binding protein-containing complex binding RNA binding nucleic acid binding pre-miRNA 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	cellular localization nitrogen compound transport regulation of cellular process nucleocytoplasmic transport transport nuclear transport negative regulation of biological process localization post-transcriptional regulation of gene expression establishment of localization in cell negative regulation of cellular process RNA localization nuclear export nucleobase-containing compound transport cellular localization nitrogen compound transport regulation of cellular process nucleocytoplasmic transport transport nuclear transport negative regulation of biological process localization post-transcriptional regulation of gene expression establishment of localization in cell negative regulation of cellular process RNA localization nuclear export nucleobase-containing compound transport negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process RNA transport negative regulation of metabolic process nucleic acid transport biological regulation pre-miRNA export from nucleus intracellular transport regulation of macromolecule metabolic process gene expression establishment of localization 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 macromolecule localization post-transcriptional gene silencing cellular process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process establishment of protein localization protein export from nucleus protein transport intracellular protein localization intracellular protein transport cell division establishment of organelle localization ribonucleoprotein complex biogenesis ribosomal subunit export from nucleus cellular component biogenesis ribosome biogenesis organelle localization cellular component organization or biogenesis ribosome localization protein localization to nucleus import into nucleus establishment of protein localization to organelle protein localization to organelle protein import into nucleus mitotic nuclear division organelle fission chromosome organization sister chromatid segregation mitotic cell cycle cellular component organization organelle organization nuclear division mitotic cell cycle process mitotic sister chromatid segregation nuclear chromosome segregation cell cycle chromosome segregation cell cycle process regulation of localization regulation of protein localization positive regulation of nucleocytoplasmic transport positive regulation of biological process positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of intracellular transport regulation of protein export from nucleus positive regulation of cellular process regulation of intracellular transport regulation of transport regulation of establishment of protein localization regulation of nucleocytoplasmic transport regulation of protein transport positive regulation of protein export from nucleus positive regulation of transport regulation of cellular localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport RNA import into nucleus snRNA import into nucleus snRNA transport nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process GTP metabolic process carbohydrate derivative metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-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	protein-containing complex ribonucleoprotein complex RNAi effector complex RISC complex membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cellular anatomical structure cytoplasmic vesicle organelle protein-containing complex ribonucleoprotein complex RNAi effector complex RISC complex membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle organelle envelope nuclear envelope nucleus endomembrane system cytosol
B, G	13-mer peptide	-	-	-
A, F	Exportin-5	small GTPase binding protein binding binding enzyme binding GTPase binding RNA binding nucleic acid binding mRNA binding RISC complex binding ribonucleoprotein complex binding protein-containing complex binding pre-miRNA binding tRNA binding nucleocytoplasmic carrier activity small GTPase binding protein binding binding enzyme binding GTPase binding RNA binding nucleic acid binding mRNA binding RISC complex binding ribonucleoprotein complex binding protein-containing complex binding pre-miRNA binding tRNA binding nucleocytoplasmic carrier activity nuclear export signal receptor activity molecular carrier activity	cellular localization nitrogen compound transport regulation of cellular process nucleocytoplasmic transport transport nuclear transport negative regulation of biological process localization post-transcriptional regulation of gene expression establishment of localization in cell negative regulation of cellular process RNA localization nuclear export nucleobase-containing compound transport cellular localization nitrogen compound transport regulation of cellular process nucleocytoplasmic transport transport nuclear transport negative regulation of biological process localization post-transcriptional regulation of gene expression establishment of localization in cell negative regulation of cellular process RNA localization nuclear export nucleobase-containing compound transport negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process RNA transport negative regulation of metabolic process nucleic acid transport biological regulation pre-miRNA export from nucleus intracellular transport regulation of macromolecule metabolic process gene expression establishment of localization 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 macromolecule localization post-transcriptional gene silencing cellular process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process establishment of protein localization protein export from nucleus protein transport intracellular protein localization intracellular protein transport nucleobase-containing compound metabolic process RNA metabolic process primary metabolic process miRNA metabolic process nucleic acid metabolic process	protein-containing complex ribonucleoprotein complex RNAi effector complex RISC complex nucleocytoplasmic transport complex RNA nuclear export complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle protein-containing complex ribonucleoprotein complex RNAi effector complex RISC complex nucleocytoplasmic transport complex RNA nuclear export complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, H	IPR002041	Ran GTPase	Family
C, H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, H	IPR005225	Small GTP-binding domain	Domain
C, H	IPR001806	Small GTPase	Family
A, F	IPR016024	Armadillo-type fold	Homologous Superfamily
A, F	IPR013598	Exportin-1/Importin-beta-like	Domain
A, F	IPR001494	Importin-beta, N-terminal domain	Domain
A, F	IPR011989	Armadillo-like helical	Homologous Superfamily
A, F	IPR045065	Exportin-1/5	Family
A, F	IPR045478	Exportin-5, C-terminal domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, F	Pharos: Q9HAV4	Microsatellite Instability kidney Wilms tumor astrocytic tumor familial idiopathic steroid-resistant nephrotic syndrome large cell medulloblastoma oligodendroglioma atypical teratoid rhabdoid tumor glioblastoma malignant ependymoma ovarian cancer medulloblastoma non-small cell lung carcinoma 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.