1I7N | pdb_00001i7n

CRYSTAL STRUCTURE ANALYSIS OF THE C DOMAIN OF SYNAPSIN II FROM RAT BRAIN

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1i7nb1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Synapsin domain	Synapsin II	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1i7nb2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Synapsin C-terminal domain	Synapsin II	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1i7na1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Synapsin domain	Synapsin II	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1i7na2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Synapsin C-terminal domain	Synapsin II	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8044550	3000094	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PreATP-grasp domain	8044549	3001680	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PreATP-grasp domain	8044549	3001680	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8044550	3000094	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	RimK	e1i7nB1	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: RimK	ECOD (1.6)
B	Synapsin	e1i7nB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Synapsin	ECOD (1.6)
A	RimK	e1i7nA1	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: RimK	ECOD (1.6)
A	Synapsin	e1i7nA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Synapsin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.470.20	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
A, B	PF02078	Synapsin pre-ATP-grasp domain (Synapsin)	Synapsin pre-ATP-grasp domain	This entry represents the pre-ATP-grasp structural domain found in synapsins, which precedes the ATP-grasp domain. The structure of the pre-ATP-grasp domain consists of alpha/beta/alpha in three layers, and is possibly a rudiment form of the Rossmann ...	This entry represents the pre-ATP-grasp structural domain found in synapsins, which precedes the ATP-grasp domain. The structure of the pre-ATP-grasp domain consists of alpha/beta/alpha in three layers, and is possibly a rudiment form of the Rossmann-fold. Synapsins are neuronal phosphoproteins that play a crucial role in the regulation of neurotransmitter release and synaptic vesicle trafficking. These proteins coat synaptic vesicles and bind to the cytoskeleton, facilitating the control of neurotransmitter release at the pre-synaptic terminal. They are also involved in the regulation of axon outgrowth and synaptogenesis. They can form oligomers and interact with various proteins, such as CAPON and NOS1, which are necessary for specific nitric-oxide functions at the presynaptic level. Additionally, Synapsin-3 binds ATP and ADP, suggesting a catalytic role in which ATP hydrolysis is involved [1].	Domain
A, B	PF02750	Synapsin, ATP binding domain (Synapsin_C)	Synapsin, ATP binding domain	Ca dependent ATP binding in this ATP grasp fold. Function unknown.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	SYNAPSIN II	cytoskeletal protein binding protein binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding cytoskeletal protein binding protein binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding calcium-dependent protein binding identical protein binding	regulated exocytosis transport secretion export from cell establishment of localization vesicle-mediated transport localization secretion by cell exocytosis cellular process calcium-ion regulated exocytosis trans-synaptic signaling regulation of biological process cellular localization regulated exocytosis transport secretion export from cell establishment of localization vesicle-mediated transport localization secretion by cell exocytosis cellular process calcium-ion regulated exocytosis trans-synaptic signaling regulation of biological process cellular localization neurotransmitter secretion signaling biological regulation cell-cell signaling neurotransmitter transport cell communication chemical synaptic transmission signal release from synapse synaptic signaling signal release anterograde trans-synaptic signaling establishment of localization in cell cellular component organization cell junction organization synapse organization cellular component organization or biogenesis regulation of localization regulation of cellular process modulation of chemical synaptic transmission regulation of secretion by cell regulation of signaling regulation of transport regulation of neurotransmitter transport regulation of secretion regulation of trans-synaptic signaling regulation of neurotransmitter secretion regulation of cell communication vesicle localization synaptic vesicle clustering synaptic vesicle cycle vesicle-mediated transport in synapse organelle localization synaptic vesicle localization	axon synapse neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection cellular anatomical structure distal axon terminal bouton cell junction neuron projection terminus SNARE complex protein-containing complex axon synapse neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection cellular anatomical structure distal axon terminal bouton cell junction neuron projection terminus SNARE complex protein-containing complex intracellular anatomical structure membrane membrane protein complex cytoplasm cell periphery plasma membrane membrane-bounded organelle extrinsic component of synaptic vesicle membrane intracellular vesicle transport vesicle membrane extrinsic component of organelle membrane endomembrane system intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane vesicle transport vesicle exocytic vesicle membrane intracellular membrane-bounded organelle cytoplasmic vesicle membrane organelle secretory vesicle organelle membrane extrinsic component of membrane exocytic vesicle glutamatergic synapse postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse Schaffer collateral - CA1 synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001359	Synapsin	Family
A, B	IPR020897	Synapsin, pre-ATP-grasp domain	Domain
A, B	IPR019736	Synapsin, phosphorylation site	PTM
A, B	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B	IPR019735	Synapsin, conserved site	Conserved Site
A, B	IPR020898	Synapsin, ATP-binding domain	Domain

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.