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- PDB-6dlv: Cryo-EM of the GTP-bound human dynamin-1 polymer assembled on the... -

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Basic information

Entry
Database: PDB / ID: 6dlv
TitleCryo-EM of the GTP-bound human dynamin-1 polymer assembled on the membrane in the super constricted state
ComponentsDynamin-1
KeywordsENDOCYTOSIS / HYDROLASE / dynamin family / gtpase / pleckstrin homology domain / membrane protein
Function / homologyDynamin, GTPase domain / Dynamin central region / Pleckstrin homology domain / Dynamin GTPase effector / PH-like domain superfamily / Dynamin, GTPase region, conserved site / GTPase effector domain / Dynamin superfamily / P-loop containing nucleoside triphosphate hydrolase / Dynamin-1 ...Dynamin, GTPase domain / Dynamin central region / Pleckstrin homology domain / Dynamin GTPase effector / PH-like domain superfamily / Dynamin, GTPase region, conserved site / GTPase effector domain / Dynamin superfamily / P-loop containing nucleoside triphosphate hydrolase / Dynamin-1 / Dynamin-type guanine nucleotide-binding (G) domain / PH domain / Dynamin family / Dynamin GTPase effector domain / Dynamin central domain / Dynamin-type guanine nucleotide-binding (G) domain signature. / PH domain profile. / GED domain profile. / Dynamin-type guanine nucleotide-binding (G) domain profile. / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Gap junction degradation / Formation of annular gap junctions / MHC class II antigen presentation / EPH-ephrin mediated repulsion of cells / Recycling pathway of L1 / Clathrin-mediated endocytosis / synaptic vesicle budding from presynaptic endocytic zone membrane / dynamin GTPase / synaptic transmission, GABAergic / dynamin family protein polymerization involved in mitochondrial fission / D2 dopamine receptor binding / varicosity / membrane coat / G protein-coupled receptor internalization / positive regulation of synaptic vesicle endocytosis / clathrin-dependent endocytosis / endosome organization / mitochondrial fission / response to amyloid-beta / membrane fusion / toxin transport / nitric-oxide synthase binding / mitochondrial membrane / adult locomotory behavior / photoreceptor inner segment / synaptic vesicle / sensory perception of sound / ephrin receptor signaling pathway / protein tetramerization / SH3 domain binding / endocytosis / receptor-mediated endocytosis / microtubule binding / microtubule / protein C-terminus binding / protein-containing complex binding / protein dimerization activity / GTPase activity / myelin sheath / GTP binding / protein kinase binding / Golgi apparatus / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / nucleus / Dynamin-1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 10.1 Å resolution
AuthorsKong, L. / Wang, H. / Fang, S. / Canagarajah, B. / Kehr, A.D. / Rice, W.J. / Hinshaw, J.E.
CitationJournal: Nature / Year: 2018
Title: Cryo-EM of the dynamin polymer assembled on lipid membrane.
Authors: Leopold Kong / Kem A Sochacki / Huaibin Wang / Shunming Fang / Bertram Canagarajah / Andrew D Kehr / William J Rice / Marie-Paule Strub / Justin W Taraska / Jenny E Hinshaw
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 2, 2018 / Release: Aug 1, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 1, 2018Structure modelrepositoryInitial release
1.1Aug 15, 2018Structure modelData collection / Database referencescitation / citation_author / pdbx_database_related_citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_database_related.db_id
1.2Aug 22, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
b: Dynamin-1
c: Dynamin-1
f: Dynamin-1
g: Dynamin-1


Theoretical massNumber of molelcules
Total (without water)343,4374
Polyers343,4374
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 15 / Rise per n subunits: 14.63 Å / Rotation per n subunits: 26.14 deg.

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Components

#1: Protein/peptide
Dynamin-1 /


Mass: 85859.148 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1, DNM / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q05193, dynamin GTPase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: GTP-bound human dynamin helical polymer encased around phosphatidylserine lipid bilayer membrane tube
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 98 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 36 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 26.14 deg. / Axial rise/subunit: 14.63 Å / Axial symmetry: C1
3D reconstructionResolution: 10.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 14322 / Symmetry type: HELICAL

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