7A17 | pdb_00007a17

Crystal structure of the 5-phosphatase domain of Synaptojanin1 bound to its substrate diC8-PI(3,4,5)P3 in complex with a nanobody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
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)
B	d7a17b_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d7a17d_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d7a17f_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Exo_endo_phos	e7a17A1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)
B	V-set_8	e7a17B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C	Exo_endo_phos	e7a17C1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)
E	Exo_endo_phos	e7a17E1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)
D	V-set_8	e7a17D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
F	V-set_8	e7a17F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV1	-	isoform 2 of synaptojanin-1	SAbDab (2025-04-25)
D	Heavy Chain	IGHV1	-	isoform 2 of synaptojanin-1	SAbDab (2025-04-25)
F	Heavy Chain	IGHV1	-	isoform 2 of synaptojanin-1	SAbDab (2025-04-25)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22669	Endonuclease/Exonuclease/phosphatase family 2 (Exo_endo_phos2)	Endonuclease/Exonuclease/phosphatase family 2	This large family of proteins includes a number of nucleases and phosphatases such as DNAase I, Exonuclease III and Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase [1-5].	Domain
C, E	PF22669	Endonuclease/Exonuclease/phosphatase family 2 (Exo_endo_phos2)	Endonuclease/Exonuclease/phosphatase family 2	This large family of proteins includes a number of nucleases and phosphatases such as DNAase I, Exonuclease III and Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Isoform 2 of Synaptojanin-1	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity phosphatidylinositol phosphate phosphatase activity catalytic activity phosphatidylinositol phosphate 4-phosphatase activity phosphatidylinositol-3-phosphate phosphatase activity phosphatidylinositol monophosphate phosphatase activity RNA binding binding nucleic acid binding phosphatidylinositol-4-phosphate phosphatase activity inositol trisphosphate phosphatase activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity phosphatidylinositol phosphate phosphatase activity catalytic activity phosphatidylinositol phosphate 4-phosphatase activity phosphatidylinositol-3-phosphate phosphatase activity phosphatidylinositol monophosphate phosphatase activity RNA binding binding nucleic acid binding phosphatidylinositol-4-phosphate phosphatase activity inositol trisphosphate phosphatase activity inositol-polyphosphate 5-phosphatase activity inositol phosphate phosphatase activity inositol-1,4,5-trisphosphate 5-phosphatase activity phosphatidylinositol bisphosphate phosphatase activity phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity phosphatidylinositol-3,5-bisphosphate phosphatase activity phosphatidylinositol phosphate 5-phosphatase activity phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity phosphatidylinositol-4,5-bisphosphate phosphatase activity phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity	localization transport neurotransmitter transport establishment of localization synaptic vesicle endocytosis import into cell cellular localization synaptic vesicle cycle vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling establishment of localization in cell cellular process localization transport neurotransmitter transport establishment of localization synaptic vesicle endocytosis import into cell cellular localization synaptic vesicle cycle vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling establishment of localization in cell cellular process endocytosis behavior multicellular organismal process system process learning learning or memory nervous system process cognition phosphatidylinositol metabolic process dephosphorylation glycerophospholipid metabolic process lipid modification primary metabolic process phospholipid metabolic process organophosphate metabolic process phosphatidylinositol dephosphorylation phospholipid dephosphorylation phosphate-containing compound metabolic process metabolic process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process positive regulation of organelle organization regulation of biological process regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of endosome organization biological regulation positive regulation of biological process regulation of organelle organization vesicle organization cellular component organization regulation of endosome organization organelle organization endosome organization cellular component organization or biogenesis endomembrane system organization positive regulation of cellular process vesicle localization establishment of organelle localization establishment of vesicle localization organelle localization synaptic vesicle localization synaptic vesicle transport polyol metabolic process alcohol metabolic process small molecule metabolic process inositol phosphate metabolic process glycerophospholipid biosynthetic process lipid biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process biosynthetic process glycerolipid biosynthetic process organophosphate biosynthetic process membrane organization synaptic vesicle uncoating protein-containing complex disassembly vesicle uncoating cellular component disassembly clathrin coat disassembly protein-containing complex organization protein depolymerization regulated exocytosis synaptic vesicle priming signaling synaptic vesicle exocytosis cell communication cellular component biogenesis synaptic signaling cellular component assembly secretion by cell signal release protein-containing complex assembly trans-synaptic signaling neurotransmitter secretion secretion export from cell cell-cell signaling chemical synaptic transmission signal release from synapse exocytosis anterograde trans-synaptic signaling exocytic process	protein-containing complex intracellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex coated membrane endomembrane system clathrin coat membrane coat cell periphery cellular anatomical structure clathrin-coated pit cytoplasm protein-containing complex intracellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex coated membrane endomembrane system clathrin coat membrane coat cell periphery cellular anatomical structure clathrin-coated pit cytoplasm clathrin coat of coated pit synapse cell junction plasma membrane region synaptic membrane axon neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection distal axon terminal bouton neuron projection terminus cytosol membrane-bounded organelle vesicle membrane organelle vesicle organelle membrane perinuclear region of cytoplasm
B	Nanobody 13015	-	-	-
C, E	Isoform 2 of Synaptojanin-1	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity phosphatidylinositol phosphate phosphatase activity catalytic activity phosphatidylinositol phosphate 4-phosphatase activity phosphatidylinositol-3-phosphate phosphatase activity phosphatidylinositol monophosphate phosphatase activity RNA binding binding nucleic acid binding phosphatidylinositol-4-phosphate phosphatase activity inositol trisphosphate phosphatase activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity phosphatidylinositol phosphate phosphatase activity catalytic activity phosphatidylinositol phosphate 4-phosphatase activity phosphatidylinositol-3-phosphate phosphatase activity phosphatidylinositol monophosphate phosphatase activity RNA binding binding nucleic acid binding phosphatidylinositol-4-phosphate phosphatase activity inositol trisphosphate phosphatase activity inositol-polyphosphate 5-phosphatase activity inositol phosphate phosphatase activity inositol-1,4,5-trisphosphate 5-phosphatase activity phosphatidylinositol bisphosphate phosphatase activity phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity phosphatidylinositol-3,5-bisphosphate phosphatase activity phosphatidylinositol phosphate 5-phosphatase activity phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity phosphatidylinositol-4,5-bisphosphate phosphatase activity phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity	localization transport neurotransmitter transport establishment of localization synaptic vesicle endocytosis import into cell cellular localization synaptic vesicle cycle vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling establishment of localization in cell cellular process localization transport neurotransmitter transport establishment of localization synaptic vesicle endocytosis import into cell cellular localization synaptic vesicle cycle vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling establishment of localization in cell cellular process endocytosis behavior multicellular organismal process system process learning learning or memory nervous system process cognition phosphatidylinositol metabolic process dephosphorylation glycerophospholipid metabolic process lipid modification primary metabolic process phospholipid metabolic process organophosphate metabolic process phosphatidylinositol dephosphorylation phospholipid dephosphorylation phosphate-containing compound metabolic process metabolic process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process positive regulation of organelle organization regulation of biological process regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of endosome organization biological regulation positive regulation of biological process regulation of organelle organization vesicle organization cellular component organization regulation of endosome organization organelle organization endosome organization cellular component organization or biogenesis endomembrane system organization positive regulation of cellular process vesicle localization establishment of organelle localization establishment of vesicle localization organelle localization synaptic vesicle localization synaptic vesicle transport polyol metabolic process alcohol metabolic process small molecule metabolic process inositol phosphate metabolic process glycerophospholipid biosynthetic process lipid biosynthetic process phospholipid biosynthetic process phosphatidylinositol biosynthetic process biosynthetic process glycerolipid biosynthetic process organophosphate biosynthetic process membrane organization synaptic vesicle uncoating protein-containing complex disassembly vesicle uncoating cellular component disassembly clathrin coat disassembly protein-containing complex organization protein depolymerization regulated exocytosis synaptic vesicle priming signaling synaptic vesicle exocytosis cell communication cellular component biogenesis synaptic signaling cellular component assembly secretion by cell signal release protein-containing complex assembly trans-synaptic signaling neurotransmitter secretion secretion export from cell cell-cell signaling chemical synaptic transmission signal release from synapse exocytosis anterograde trans-synaptic signaling exocytic process	protein-containing complex intracellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex coated membrane endomembrane system clathrin coat membrane coat cell periphery cellular anatomical structure clathrin-coated pit cytoplasm protein-containing complex intracellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex coated membrane endomembrane system clathrin coat membrane coat cell periphery cellular anatomical structure clathrin-coated pit cytoplasm clathrin coat of coated pit synapse cell junction plasma membrane region synaptic membrane axon neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection distal axon terminal bouton neuron projection terminus cytosol membrane-bounded organelle vesicle membrane organelle vesicle organelle membrane perinuclear region of cytoplasm
D	Nanobody 13015	-	-	-
F	Nanobody 13015	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR034971	Synaptojanin-1, RNA recognition motif	Domain
A	IPR002013	SAC domain	Domain
A	IPR000504	RNA recognition motif domain	Domain
A	IPR000300	Inositol polyphosphate-related phosphatase	Domain
A	IPR046985	Inositol 5-phosphatase	Family
A	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	Homologous Superfamily
A	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
A	IPR015047	Synaptojanin-1/2, RNA recognition motif	Domain
C, E	IPR034971	Synaptojanin-1, RNA recognition motif	Domain
C, E	IPR002013	SAC domain	Domain
C, E	IPR000504	RNA recognition motif domain	Domain
C, E	IPR000300	Inositol polyphosphate-related phosphatase	Domain
C, E	IPR046985	Inositol 5-phosphatase	Family
C, E	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
C, E	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	Homologous Superfamily
C, E	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
C, E	IPR015047	Synaptojanin-1/2, RNA recognition motif	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O43426	early-onset Parkinson disease 20 developmental and epileptic encephalopathy, 53 Parkinson disease pilocytic astrocytoma astrocytic tumor epilepsy intellectual disability malignant ependymoma neurodegenerative disease primitive neuroectodermal tumor atypical juvenile parkinsonism Down syndrome Epileptic encephalopathy large cell medulloblastoma malignant glioma early-onset Parkinson disease 20 developmental and epileptic encephalopathy, 53 Parkinson disease pilocytic astrocytoma astrocytic tumor epilepsy intellectual disability malignant ependymoma neurodegenerative disease primitive neuroectodermal tumor atypical juvenile parkinsonism Down syndrome Epileptic encephalopathy large cell medulloblastoma malignant glioma oligodendroglioma Pick disease tuberculosis atypical teratoid rhabdoid tumor glioblastoma lung cancer medulloblastoma ovarian cancer
C, E	Pharos: O43426	early-onset Parkinson disease 20 developmental and epileptic encephalopathy, 53 Parkinson disease pilocytic astrocytoma astrocytic tumor epilepsy intellectual disability malignant ependymoma neurodegenerative disease primitive neuroectodermal tumor atypical juvenile parkinsonism Down syndrome Epileptic encephalopathy large cell medulloblastoma malignant glioma early-onset Parkinson disease 20 developmental and epileptic encephalopathy, 53 Parkinson disease pilocytic astrocytoma astrocytic tumor epilepsy intellectual disability malignant ependymoma neurodegenerative disease primitive neuroectodermal tumor atypical juvenile parkinsonism Down syndrome Epileptic encephalopathy large cell medulloblastoma malignant glioma oligodendroglioma Pick disease tuberculosis atypical teratoid rhabdoid tumor glioblastoma lung cancer medulloblastoma ovarian cancer

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.