6DLU | pdb_00006dlu

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

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)
B [auth P]	SCOP2B Superfamily	Dynamin stalk-like	8058469	3002023	SCOP2B (2022-06-29)
B [auth P]	SCOP2B Superfamily	PH domain-like	8058467	3000134	SCOP2B (2022-06-29)
B [auth P]	SCOP2B Superfamily	Ras-like P-loop GTPases	8058465	3002022	SCOP2B (2022-06-29)
B [auth P]	SCOP2B Superfamily	Dynamin stalk-like	8058469	3002023	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Dynamin stalk-like	8058469	3002023	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)
A [auth B]	SCOP2B Superfamily	Ras-like P-loop GTPases	8058465	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)
B [auth P]	PH	e6dluP1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PH	ECOD (1.6)
B [auth P]	Dynamin_M	e6dluP3	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 [auth P]	Dynamin_N	e6dluP2	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 [auth B]	PH	e6dluB1	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PH	ECOD (1.6)
A [auth B]	Dynamin_M	e6dluB3	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 [auth B]	Dynamin_N	e6dluB2	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)
B [auth P]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth P]	PF01031	Dynamin central region (Dynamin_M)	Dynamin central region	-	Family
A [auth B], B [auth P]	PF00350	Dynamin family (Dynamin_N)	Dynamin family		Domain
A [auth B], B [auth P]	PF02212	Dynamin GTPase effector domain (GED)	Dynamin GTPase effector domain	-	Family
A [auth B], B [auth P]	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 P]	Dynamin-1	RNA binding 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 RNA binding 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 cytoskeletal protein binding microtubule binding protein binding tubulin binding GDP binding identical protein binding protein homodimerization activity protein dimerization activity kinase binding enzyme binding protein kinase binding phosphatidylinositol-3,4,5-trisphosphate 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	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 protein-containing complex organization protein homotetramerization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization 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 clathrin coat assembly involved in endocytosis clathrin coat assembly clathrin-dependent endocytosis regulation of cellular component size regulation of vesicle size biological regulation regulation of biological quality regulation of anatomical structure size endosome organization endomembrane system organization	cellular anatomical structure clathrin-coated pit membrane endomembrane system extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery cellular anatomical structure clathrin-coated pit membrane endomembrane system extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane presynapse synapse cell junction intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle cytoplasm endocytic vesicle cell projection polymeric cytoskeletal fiber intracellular membraneless organelle cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton chromaffin granule secretory granule secretory vesicle

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], B [auth P]	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 R01GM157729.