6MDO | pdb_00006mdo

The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus within the 20S supercomplex (focused refinement on D1/D2 rings, class 1)

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8044318	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8044318	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8044318	3002019	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RecA-like P-loop NTPases	8044318	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8044318	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8044318	3002019	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)
A	KOG0741	e6mdoA3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: KOG0741	ECOD (1.6)
A	PRK03992	e6mdoA2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK03992	ECOD (1.6)
A	AAA	e6mdoA4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA	ECOD (1.6)
A	AAA_11_1	e6mdoA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11_1	ECOD (1.6)
D	KOG0741	e6mdoD3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: KOG0741	ECOD (1.6)
D	PRK03992	e6mdoD2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK03992	ECOD (1.6)
D	AAA	e6mdoD4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA	ECOD (1.6)
D	AAA_11_1	e6mdoD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11_1	ECOD (1.6)
E	KOG0741	e6mdoE4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: KOG0741	ECOD (1.6)
E	PRK03992	e6mdoE3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK03992	ECOD (1.6)
E	AAA	e6mdoE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA	ECOD (1.6)
E	AAA_11_1	e6mdoE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11_1	ECOD (1.6)
F	KOG0741	e6mdoF2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: KOG0741	ECOD (1.6)
F	AAA_11_1	e6mdoF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11_1	ECOD (1.6)
C	KOG0741	e6mdoC3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: KOG0741	ECOD (1.6)
C	PRK03992	e6mdoC2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK03992	ECOD (1.6)
C	AAA	e6mdoC4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA	ECOD (1.6)
C	AAA_11_1	e6mdoC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11_1	ECOD (1.6)
B	KOG0741	e6mdoB3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: KOG0741	ECOD (1.6)
B	PRK03992	e6mdoB2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK03992	ECOD (1.6)
B	AAA	e6mdoB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA	ECOD (1.6)
B	AAA_11_1	e6mdoB4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF17862	AAA+ lid domain (AAA_lid_3)	AAA+ lid domain	This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.	Domain
A, B, C, D, E A, B, C, D, E, F	PF00004	ATPase family associated with various cellular activities (AAA) (AAA)	ATPase family associated with various cellular activities (AAA)	AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].	Domain
A, B, C, D, E A, B, C, D, E, F	PF21964	NSF, AAA+ ATPase lid domain (NSF_ATPase_lid)	NSF, AAA+ ATPase lid domain	This entry represents the ATPase lid domain of the second AAA+ ATP-binding domain (also known as D2) of NSF proteins [1], found at the C-terminal. NFS proteins are essential membrane fusion events. They play the role of a chaperone by activating SNAP ...	This entry represents the ATPase lid domain of the second AAA+ ATP-binding domain (also known as D2) of NSF proteins [1], found at the C-terminal. NFS proteins are essential membrane fusion events. They play the role of a chaperone by activating SNAP receptor proteins (SNAREs) so that they can participate in membrane fusion [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth H]	Synaptosomal-associated protein 25	SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity monoatomic cation transmembrane transporter activity gated channel activity monoatomic ion channel activity potassium ion transmembrane transporter activity voltage-gated channel activity voltage-gated monoatomic ion channel activity potassium channel activity voltage-gated monoatomic cation channel activity monoatomic cation channel activity passive transmembrane transporter activity voltage-gated potassium channel activity SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity monoatomic cation transmembrane transporter activity gated channel activity monoatomic ion channel activity potassium ion transmembrane transporter activity voltage-gated channel activity voltage-gated monoatomic ion channel activity potassium channel activity voltage-gated monoatomic cation channel activity monoatomic cation channel activity passive transmembrane transporter activity voltage-gated potassium channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity protein binding binding protein domain specific binding syntaxin-1 binding SNARE binding syntaxin binding transmembrane transporter binding lipid binding cytoskeletal protein binding myosin binding calcium-dependent protein binding	positive regulation of cell communication regulation of localization regulation of cellular process regulation of hormone secretion signaling transport positive regulation of biological process positive regulation of secretion by cell hormone secretion cell communication localization positive regulation of hormone secretion regulation of secretion by cell secretion by cell positive regulation of secretion positive regulation of cell communication regulation of localization regulation of cellular process regulation of hormone secretion signaling transport positive regulation of biological process positive regulation of secretion by cell hormone secretion cell communication localization positive regulation of hormone secretion regulation of secretion by cell secretion by cell positive regulation of secretion signal release regulation of biological quality positive regulation of cellular process regulation of signaling regulation of biological process regulation of transport secretion regulation of hormone levels biological regulation export from cell cell-cell signaling establishment of localization regulation of secretion positive regulation of transport regulation of cell communication hormone transport cellular process positive regulation of signaling establishment of protein localization regulation of protein localization macromolecule localization regulation of establishment of protein localization intracellular protein localization membrane organization protein-containing complex organization membrane fusion organelle membrane fusion vesicle-mediated transport cellular component organization cellular component biogenesis vesicle organization organelle fusion organelle organization cellular component assembly protein-containing complex assembly SNARE complex assembly cellular component organization or biogenesis vesicle fusion multicellular organismal process axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development developmental process plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development cellular localization establishment of localization in cell intracellular transport endosomal transport regulated exocytosis synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse synaptic signaling calcium-ion regulated exocytosis calcium ion-regulated exocytosis of neurotransmitter trans-synaptic signaling neurotransmitter secretion neurotransmitter transport chemical synaptic transmission signal release from synapse exocytosis anterograde trans-synaptic signaling regulation of cellular component organization cell junction assembly regulation of synapse structure or activity regulation of synapse assembly synapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly establishment of organelle localization dense core granule localization organelle localization presynaptic dense core vesicle exocytosis secretory granule localization vesicle localization establishment of vesicle localization neuronal dense core vesicle exocytosis dense core granule exocytosis synaptic vesicle priming exocytic process behavior locomotory behavior system process learning or memory long-term memory nervous system process cognition memory learning associative learning endomembrane system organization vesicle fusion to plasma membrane synaptic vesicle fusion to presynaptic active zone membrane synaptic vesicle membrane organization nitrogen compound transport positive regulation of establishment of protein localization positive regulation of insulin secretion regulation of peptide hormone secretion positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion positive regulation of protein localization regulation of peptide secretion protein localization to extracellular region positive regulation of protein transport peptide secretion amide transport positive regulation of peptide secretion regulation of peptide transport regulation of protein transport positive regulation of protein secretion peptide transport protein transport regulation of insulin secretion peptide hormone secretion insulin secretion regulation of neuron projection development regulation of cell projection organization regulation of plasma membrane bounded cell projection organization modulation of chemical synaptic transmission long-term synaptic potentiation regulation of synaptic plasticity positive regulation of synaptic transmission regulation of trans-synaptic signaling	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane photoreceptor inner segment intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane photoreceptor inner segment intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cell periphery presynapse synapse cell junction plasma membrane presynaptic membrane plasma membrane region synaptic membrane cytoplasm glutamatergic synapse neuron projection membrane-bounded organelle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system trans-Golgi network SNARE complex protein-containing complex synaptobrevin 2-SNAP-25-syntaxin-1a complex membrane protein complex synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex perinuclear region of cytoplasm somatodendritic compartment cell body neuronal cell body axon synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex transport vesicle intracellular vesicle cytoplasmic vesicle synaptic vesicle secretory vesicle vesicle exocytic vesicle actin-based cell projection filopodium growth cone distal axon axonal growth cone site of polarized growth cell cortex axon terminus terminal bouton neuron projection terminus ribbon synapse voltage-gated potassium channel complex plasma membrane protein complex potassium channel complex cation channel complex transporter complex transmembrane transporter complex monoatomic ion channel complex endosome extrinsic component of plasma membrane extrinsic component of synaptic membrane extrinsic component of presynaptic membrane extrinsic component of membrane BLOC complex intracellular protein-containing complex BLOC-1 complex
A, B, C, D, E A, B, C, D, E, F	Vesicle-fusing ATPase	syntaxin-1 binding protein binding binding SNARE binding syntaxin binding PDZ domain binding protein domain specific binding protein-containing complex destabilizing activity ATP-dependent protein disaggregase activity ATP-dependent activity ionotropic glutamate receptor binding signaling receptor binding glutamate receptor binding adenyl ribonucleotide binding syntaxin-1 binding protein binding binding SNARE binding syntaxin binding PDZ domain binding protein domain specific binding protein-containing complex destabilizing activity ATP-dependent protein disaggregase activity ATP-dependent activity ionotropic glutamate receptor binding signaling receptor binding glutamate receptor 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 kinase binding enzyme binding protein kinase binding protein-containing complex binding pyrophosphatase activity ATP hydrolysis 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 cation binding metal ion binding identical protein binding	Golgi to plasma membrane transport establishment of protein localization cellular localization protein localization to cell periphery nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to membrane protein localization to plasma membrane establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport Golgi to plasma membrane transport establishment of protein localization cellular localization protein localization to cell periphery nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to membrane protein localization to plasma membrane establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane localization protein transport macromolecule localization cellular process intracellular protein localization Golgi vesicle transport regulation of cellular process catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process intra-Golgi vesicle-mediated transport regulation of signaling signaling regulation of receptor recycling receptor recycling receptor metabolic process positive regulation of receptor recycling positive regulation of signaling monoatomic ion transport potassium ion transport monoatomic cation transport metal ion transport intracellular transport establishment of localization in cell intracellular protein transport cellular component disassembly protein-containing complex organization SNARE complex disassembly protein-containing complex disassembly cellular component organization cellular component organization or biogenesis	midbody cellular anatomical structure membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle Golgi stack cytoplasm cytosol midbody cellular anatomical structure membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle Golgi stack cytoplasm cytosol cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth H]	IPR000727	Target SNARE coiled-coil homology domain	Domain
G [auth H]	IPR039077	SNAP25, N-terminal SNARE motif, chordates	Domain
G [auth H]	IPR000928	SNAP-25 domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR004201	CDC48, domain 2	Domain
A, B, C, D, E A, B, C, D, E, F	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003959	ATPase, AAA-type, core	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR029067	CDC48 domain 2-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR039812	Vesicle-fusing ATPase	Family
A, B, C, D, E A, B, C, D, E, F	IPR054419	NSF, AAA+ ATPase lid domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR003338	CDC48, N-terminal subdomain	Domain