7MNY | pdb_00007mny

Crystal Structure of Nup358/RanBP2 Ran-binding domain 3 in complex with Ran-GPPNHP

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
K	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	3002022	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	3002022	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	3002022	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057412	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)
L	Thaumatin	e7mnyL1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
J	Thaumatin	e7mnyJ1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
H	Thaumatin	e7mnyH1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
F	Thaumatin	e7mnyF1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
D	Thaumatin	e7mnyD1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
B	Thaumatin	e7mnyB1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
K	Thaumatin	e7mnyK1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
I	Thaumatin	e7mnyI1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
G	Thaumatin	e7mnyG1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
E	Thaumatin	e7mnyE1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
C	Thaumatin	e7mnyC1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)
A	Thaumatin	e7mnyA1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Thaumatin	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L	PF00638	RanBP1 domain (Ran_BP1)	RanBP1 domain		Domain
A, C, E, G, I A, C, E, G, I, K	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L	E3 SUMO-protein ligase RanBP2	small GTPase binding protein binding binding enzyme binding GTPase binding enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity kinase regulator activity protein-macromolecule adaptor activity molecular adaptor activity aminoacyltransferase activity small GTPase binding protein binding binding enzyme binding GTPase binding enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity kinase regulator activity protein-macromolecule adaptor activity molecular adaptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity SUMO ligase activity ubiquitin-like protein ligase activity protein-containing complex binding	localization centrosome localization microtubule organizing center localization cellular process protein folding biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation cellular localization localization centrosome localization microtubule organizing center localization cellular process protein folding biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport establishment of localization peptidyl-lysine modification protein sumoylation macromolecule modification protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal nuclear export establishment of protein localization NLS-bearing protein import into nucleus protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport macromolecule localization protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport response to amine response to stimulus response to chemical response to nitrogen compound response to amphetamine regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary 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 regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation regulation of macromolecule 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 regulation of metabolic process negative regulation of RNA metabolic process	cellular anatomical structure membrane membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system nuclear membrane organelle membrane cytoplasmic periphery of the nuclear pore complex cellular anatomical structure membrane membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system nuclear membrane organelle membrane cytoplasmic periphery of the nuclear pore complex perinuclear region of cytoplasm cytoplasm cytosol protein-containing complex nuclear protein-containing complex nuclear pore membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nuclear pore nuclear basket catalytic complex SUMO ligase complex transferase complex inclusion body nuclear inclusion body nuclear outer membrane-endoplasmic reticulum membrane network annulate lamellae nuclear pore cytoplasmic filaments
A, C, E, G, I A, C, E, G, I, K	GTP-binding nuclear protein Ran	chromatin binding binding protein heterodimerization activity protein binding protein dimerization activity RNA binding nucleic acid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding chromatin binding binding protein heterodimerization activity protein binding protein dimerization activity RNA 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 cell adhesion molecule binding cadherin binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	cellular process cell cycle mitotic cell cycle 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 cellular process cell cycle mitotic cell cycle 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 regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process establishment of organelle localization ribonucleoprotein complex biogenesis ribosomal subunit export from nucleus cellular component biogenesis ribosome biogenesis ribosomal small subunit export from nucleus organelle localization cellular component organization or biogenesis ribosome localization establishment of protein localization protein export from nucleus protein transport intracellular protein localization intracellular protein transport viral process ribosomal large subunit export from nucleus 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 cellular component organization organelle organization nuclear division mitotic cell cycle process mitotic sister chromatid segregation nuclear chromosome segregation chromosome segregation cell cycle process protein localization to nucleolus regulation of localization 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 transport positive regulation of protein localization to nucleus 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 microtubule cytoskeleton organization mitotic spindle organization microtubule-based process cytoskeleton organization microtubule cytoskeleton organization involved in mitosis spindle organization nucleobase-containing compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process 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 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 small molecule metabolic process nucleoside triphosphate metabolic process phosphorus metabolic process purine ribonucleotide metabolic process	midbody cellular anatomical structure membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle membraneless organelle midbody cellular anatomical structure membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle membraneless organelle nuclear lumen membrane pigment granule intracellular vesicle melanosome cytoplasmic vesicle cytoplasm vesicle protein-containing complex nucleocytoplasmic transport complex RNA nuclear export complex organelle envelope nuclear envelope endomembrane system extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle microtubule organizing center cytoskeleton centriole microtubule cytoskeleton cytosol nuclear protein-containing complex nuclear pore nucleoplasm chromatin chromosome endosome recycling endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L	IPR022011	Nup358/RanBP2 E3 ligase domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR029000	Cyclophilin-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR002130	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR011993	PH-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR019734	Tetratricopeptide repeat	Repeat
B, D, F, H, J B, D, F, H, J, L	IPR020892	Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site	Conserved Site
B, D, F, H, J B, D, F, H, J, L	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR000156	Ran binding domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR001876	Zinc finger, RanBP2-type	Domain
B, D, F, H, J B, D, F, H, J, L	IPR045255	Ran binding protein RanBP1-like	Family
A, C, E, G, I A, C, E, G, I, K	IPR002041	Ran GTPase	Family
A, C, E, G, I A, C, E, G, I, K	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR005225	Small GTP-binding domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR001806	Small GTPase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H, J B, D, F, H, J, L	: P49792	familial acute necrotizing encephalopathy inflammatory myofibroblastic tumor psoriasis acute necrotizing encephalitis breast carcinoma ectodermal dysplasia 10B, hypohidrotic/hair/tooth type, autosomal recessive hereditary spastic paraplegia lung cancer ovarian cancer tuberculosis adrenal cortex carcinoma dermatomyositis ENCEPHALOPATHY, ACUTE, INFECTION-INDUCED, SUSCEPTIBILITY TO, 3 glioblastoma hypohidrotic ectodermal dysplasia familial acute necrotizing encephalopathy inflammatory myofibroblastic tumor psoriasis acute necrotizing encephalitis breast carcinoma ectodermal dysplasia 10B, hypohidrotic/hair/tooth type, autosomal recessive hereditary spastic paraplegia lung cancer ovarian cancer tuberculosis adrenal cortex carcinoma dermatomyositis ENCEPHALOPATHY, ACUTE, INFECTION-INDUCED, SUSCEPTIBILITY TO, 3 glioblastoma hypohidrotic ectodermal dysplasia malignant mesothelioma plasma cell myeloma atypical teratoid rhabdoid tumor ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant myopathy
A, C, E, G, I A, C, E, G, I, K	: 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

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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.