5A3F | pdb_00005a3f

Crystal structure of the dynamin tetramer

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Dynamin stalk-like	8054367	3002023	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8054366	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Dynamin stalk-like	8054367	3002023	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Dynamin stalk-like	8054367	3002023	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Dynamin stalk-like	8054367	3002023	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8054366	3002022	SCOP2B (2022-06-29)
B	SCOP2 Family	Dynamin G domain-like	8050012	4004047	SCOP2 (2022-06-29)
B	SCOP2 Family	Dynamin stalk region-like	8054365	4004048	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ras-like P-loop GTPases	8054366	3002022	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Dynamin stalk-like	8054367	3002023	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Dynamin stalk-like	8054367	3002023	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Dynamin stalk-like	8054367	3002023	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8054366	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)
D	Dynamin_M	e5a3fD1	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: Dynamin_M	ECOD (1.6)
D	Dynamin_N	e5a3fD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Dynamin_N	ECOD (1.6)
C	PH	e5a3fC1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PH	ECOD (1.6)
C	Dynamin_M	e5a3fC3	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: Dynamin_M	ECOD (1.6)
C	Dynamin_N	e5a3fC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Dynamin_N	ECOD (1.6)
B	Dynamin_M	e5a3fB2	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: Dynamin_M	ECOD (1.6)
B	Dynamin_N	e5a3fB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Dynamin_N	ECOD (1.6)
A	PH	e5a3fA3	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PH	ECOD (1.6)
A	Dynamin_M	e5a3fA1	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: Dynamin_M	ECOD (1.6)
A	Dynamin_N	e5a3fA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Dynamin_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.120.1240	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Dynamin, middle domain	CATH (4.3.0)
C	1.20.120.1240	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Dynamin, middle domain	CATH (4.3.0)
C	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
B	1.20.120.1240	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Dynamin, middle domain	CATH (4.3.0)
A	1.20.120.1240	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Dynamin, middle domain	CATH (4.3.0)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01031	Dynamin central region (Dynamin_M)	Dynamin central region	-	Family
A, B, C, D	PF00350	Dynamin family (Dynamin_N)	Dynamin family		Domain
A, B, C, D	PF02212	Dynamin GTPase effector domain (GED)	Dynamin GTPase effector domain	-	Family
A, B, C, D	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, B, C, D	DYNAMIN 3	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 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 cytoskeletal protein binding microtubule binding protein 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	localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport establishment of organelle localization vesicle budding from membrane cellular localization synaptic vesicle cycle presynaptic endocytosis localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport establishment of organelle localization vesicle budding from membrane cellular localization synaptic vesicle cycle presynaptic endocytosis vesicle-mediated transport in synapse cellular component organization vesicle organization synaptic vesicle recycling organelle localization establishment of localization in cell synaptic vesicle budding cellular component organization or biogenesis synaptic vesicle localization synaptic vesicle endocytosis membrane organization vesicle localization establishment of vesicle localization synaptic vesicle budding from presynaptic endocytic zone membrane organelle organization synaptic vesicle transport cellular component biogenesis filopodium assembly cellular component assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cell projection assembly developmental process multicellular organismal process nervous system development multicellular organism development cell junction organization cell junction assembly anatomical structure development synapse organization synapse assembly system development	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane presynapse extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane presynapse synapse cell junction intracellular anatomical structure cytoplasm neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse dendrite dendritic tree postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse perinuclear region of cytoplasm polymeric cytoskeletal fiber intracellular membraneless organelle intracellular organelle cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9UQ16	osteosarcoma pilocytic astrocytoma progressive supranuclear palsy ulcerative colitis Alzheimer disease Crohn disease gastric carcinoma kidney neoplasm lung cancer malignant glioma medulloblastoma ovarian cancer pituitary cancer subependymal giant cell astrocytoma uterine corpus leiomyoma osteosarcoma pilocytic astrocytoma progressive supranuclear palsy ulcerative colitis Alzheimer disease Crohn disease gastric carcinoma kidney neoplasm lung cancer malignant glioma medulloblastoma ovarian cancer pituitary cancer subependymal giant cell astrocytoma uterine corpus leiomyoma astrocytic tumor exocrine pancreatic carcinoma glioblastoma large cell medulloblastoma lung carcinoma Malignant neoplasm of kidney non-small cell lung carcinoma Pick disease primitive neuroectodermal tumor tuberculosis atypical teratoid rhabdoid tumor gastric cancer kidney cancer lung adenocarcinoma malignant ependymoma malignant pancreatic neoplasm

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.