6DLV

Cryo-EM of the GTP-bound human dynamin-1 polymer assembled on the membrane in the super constricted state

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)
A [auth b]	SCOP2B Superfamily	Dynamin stalk-like	8058469	3002023	SCOP2B (2022-06-29)
A [auth b]	SCOP2B Superfamily	Ras-like P-loop GTPases	8058465	3002022	SCOP2B (2022-06-29)
A [auth b]	SCOP2B Superfamily	Dynamin stalk-like	8058469	3002023	SCOP2B (2022-06-29)
A [auth b]	SCOP2B Superfamily	PH domain-like	8058467	3000134	SCOP2B (2022-06-29)
B [auth c]	SCOP2B Superfamily	Dynamin stalk-like	8058469	3002023	SCOP2B (2022-06-29)
B [auth c]	SCOP2B Superfamily	Ras-like P-loop GTPases	8058465	3002022	SCOP2B (2022-06-29)
B [auth c]	SCOP2B Superfamily	Dynamin stalk-like	8058469	3002023	SCOP2B (2022-06-29)
B [auth c]	SCOP2B Superfamily	PH domain-like	8058467	3000134	SCOP2B (2022-06-29)
C [auth f]	SCOP2B Superfamily	Dynamin stalk-like	8058469	3002023	SCOP2B (2022-06-29)
C [auth f]	SCOP2B Superfamily	PH domain-like	8058467	3000134	SCOP2B (2022-06-29)
C [auth f]	SCOP2B Superfamily	Dynamin stalk-like	8058469	3002023	SCOP2B (2022-06-29)
C [auth f]	SCOP2B Superfamily	Ras-like P-loop GTPases	8058465	3002022	SCOP2B (2022-06-29)
D [auth g]	SCOP2B Superfamily	PH domain-like	8058467	3000134	SCOP2B (2022-06-29)
D [auth g]	SCOP2B Superfamily	Ras-like P-loop GTPases	8058465	3002022	SCOP2B (2022-06-29)
D [auth g]	SCOP2B Superfamily	Dynamin stalk-like	8058469	3002023	SCOP2B (2022-06-29)
D [auth g]	SCOP2B Superfamily	Dynamin stalk-like	8058469	3002023	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 [auth b]	PF00169	e6dlvb2	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PF00169	ECOD (1.6)
A [auth b]	PF01031,PF02212	e6dlvb3	A: alpha bundles	X: Middle and GTPase effector domains in dynamin-related proteins (From Topology)	H: Middle and GTPase effector domains in dynamin-related proteins (From Topology)	T: Middle and GTPase effector domains in dynamin-related proteins	F: PF01031,PF02212	ECOD (1.6)
A [auth b]	PF00350,PF01031	e6dlvb1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00350,PF01031	ECOD (1.6)
B [auth c]	PF00169	e6dlvc3	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PF00169	ECOD (1.6)
B [auth c]	PF01031,PF02212	e6dlvc2	A: alpha bundles	X: Middle and GTPase effector domains in dynamin-related proteins (From Topology)	H: Middle and GTPase effector domains in dynamin-related proteins (From Topology)	T: Middle and GTPase effector domains in dynamin-related proteins	F: PF01031,PF02212	ECOD (1.6)
B [auth c]	PF00350,PF01031	e6dlvc1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00350,PF01031	ECOD (1.6)
C [auth f]	PF00169	e6dlvf2	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PF00169	ECOD (1.6)
C [auth f]	PF01031,PF02212	e6dlvf1	A: alpha bundles	X: Middle and GTPase effector domains in dynamin-related proteins (From Topology)	H: Middle and GTPase effector domains in dynamin-related proteins (From Topology)	T: Middle and GTPase effector domains in dynamin-related proteins	F: PF01031,PF02212	ECOD (1.6)
C [auth f]	PF00350,PF01031	e6dlvf3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00350,PF01031	ECOD (1.6)
D [auth g]	PF00169	e6dlvg3	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PF00169	ECOD (1.6)
D [auth g]	PF01031,PF02212	e6dlvg2	A: alpha bundles	X: Middle and GTPase effector domains in dynamin-related proteins (From Topology)	H: Middle and GTPase effector domains in dynamin-related proteins (From Topology)	T: Middle and GTPase effector domains in dynamin-related proteins	F: PF01031,PF02212	ECOD (1.6)
D [auth g]	PF00350,PF01031	e6dlvg1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00350,PF01031	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth b], B [auth c], C [auth f], D [auth g]	PF00350	Dynamin family (Dynamin_N)	Dynamin family	-	Domain
A [auth b], B [auth c], C [auth f], D [auth g]	PF02212	Dynamin GTPase effector domain (GED)	Dynamin GTPase effector domain	-	Family
A [auth b], B [auth c], C [auth f], D [auth g]	PF00169	PH domain (PH)	PH domain	PH stands for pleckstrin homology.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth b], B [auth c], C [auth f], D [auth g]	Dynamin-1	cytoskeletal protein binding microtubule binding protein binding binding tubulin 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 identical protein binding RNA binding cytoskeletal protein binding microtubule binding protein binding binding tubulin 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 identical protein binding RNA binding organic cyclic compound 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 phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding GDP binding protein homodimerization activity protein dimerization activity kinase binding enzyme binding protein kinase binding phosphatidylinositol-3,4,5-trisphosphate binding	localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport membrane organization cellular component organization membrane fission vesicle scission cellular component organization or biogenesis localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport membrane organization cellular component organization membrane fission vesicle scission cellular component organization or biogenesis establishment of organelle localization vesicle budding from membrane cellular localization synaptic vesicle cycle presynaptic endocytosis vesicle-mediated transport in synapse vesicle organization synaptic vesicle recycling organelle localization establishment of localization in cell synaptic vesicle budding synaptic vesicle localization synaptic vesicle endocytosis vesicle localization establishment of vesicle localization synaptic vesicle budding from presynaptic endocytic zone membrane organelle organization synaptic vesicle transport trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process modulation of chemical synaptic transmission signaling biological regulation cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication endosome organization endomembrane system organization protein-containing complex organization protein homotetramerization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization clathrin coat assembly involved in endocytosis clathrin coat assembly clathrin-dependent endocytosis regulation of cellular component size regulation of vesicle size regulation of biological quality regulation of anatomical structure size	clathrin-coated pit membrane cellular anatomical entity endomembrane system presynaptic endocytic zone synapse plasma membrane presynaptic membrane synaptic membrane cell periphery presynapse presynaptic endocytic zone membrane cell junction plasma membrane region clathrin-coated pit membrane cellular anatomical entity endomembrane system presynaptic endocytic zone synapse plasma membrane presynaptic membrane synaptic membrane cell periphery presynapse presynaptic endocytic zone membrane cell junction plasma membrane region photoreceptor inner segment extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle cytoplasm endocytic vesicle glutamatergic synapse membrane coat protein-containing complex membrane protein complex coated membrane polymeric cytoskeletal fiber cytoskeleton intracellular non-membrane-bounded organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton non-membrane-bounded organelle chromaffin granule secretory granule secretory vesicle photoreceptor ribbon synapse ribbon synapse cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth b], B [auth c], C [auth f], D [auth g]	IPR020850	GTPase effector domain	Domain
A [auth b], B [auth c], C [auth f], D [auth g]	IPR001401	Dynamin, GTPase domain	Domain
A [auth b], B [auth c], C [auth f], D [auth g]	IPR045063	Dynamin, N-terminal	Domain
A [auth b], B [auth c], C [auth f], D [auth g]	IPR019762	Dynamin, GTPase region, conserved site	Conserved Site
A [auth b], B [auth c], C [auth f], D [auth g]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth b], B [auth c], C [auth f], D [auth g]	IPR001849	Pleckstrin homology domain	Domain
A [auth b], B [auth c], C [auth f], D [auth g]	IPR030381	Dynamin-type guanine nucleotide-binding (G) domain	Domain
A [auth b], B [auth c], C [auth f], D [auth g]	IPR011993	PH-like domain superfamily	Homologous Superfamily
A [auth b], B [auth c], C [auth f], D [auth g]	IPR003130	Dynamin GTPase effector	Domain
A [auth b], B [auth c], C [auth f], D [auth g]	IPR000375	Dynamin stalk domain	Domain
A [auth b], B [auth c], C [auth f], D [auth g]	IPR022812	Dynamin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth b], B [auth c], C [auth f], D [auth g]	Pharos: Q05193	developmental and epileptic encephalopathy, 31 Lennox-Gastaut syndrome epilepsy medulloblastoma Pick disease psoriasis astrocytic tumor Early infantile epileptic encephalopathy with suppression bursts facioscapulohumeral muscular dystrophy interstitial lung disease malignant glioma pilocytic astrocytoma schizophrenia atypical teratoid rhabdoid tumor dog disease developmental and epileptic encephalopathy, 31 Lennox-Gastaut syndrome epilepsy medulloblastoma Pick disease psoriasis astrocytic tumor Early infantile epileptic encephalopathy with suppression bursts facioscapulohumeral muscular dystrophy interstitial lung disease malignant glioma pilocytic astrocytoma schizophrenia atypical teratoid rhabdoid tumor dog disease glioblastoma invasive ductal breast carcinoma lung carcinoma malignant mesothelioma oligodendroglioma primitive neuroectodermal tumor West syndrome developmental and epileptic encephalopathy ductal breast carcinoma in situ intellectual disability large cell medulloblastoma malignant ependymoma

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 R01GM133198.