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

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Basic information

Entry
Database: PDB / ID: 6dlu
TitleCryo-EM of the GMPPCP-bound human dynamin-1 polymer assembled on the membrane in the constricted state
ComponentsDynamin-1
KeywordsENDOCYTOSIS / HYDROLASE / dynamin family / gtpase / pleckstrin homology domain / membrane protein
Function / homologyDynamin-1 / PH-like domain superfamily / Dynamin GTPase effector / GTPase effector domain / Dynamin superfamily / P-loop containing nucleoside triphosphate hydrolase / Pleckstrin homology domain / Dynamin-type guanine nucleotide-binding (G) domain / PH domain / Dynamin family ...Dynamin-1 / PH-like domain superfamily / Dynamin GTPase effector / GTPase effector domain / Dynamin superfamily / P-loop containing nucleoside triphosphate hydrolase / Pleckstrin homology domain / Dynamin-type guanine nucleotide-binding (G) domain / PH domain / Dynamin family / Dynamin central region / Dynamin GTPase effector domain / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin, GTPase domain / 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 / Dynamin central domain / Dynamin, GTPase region, conserved site / postsynaptic endocytic zone membrane / synaptic vesicle budding from presynaptic endocytic zone membrane / dynamin GTPase / presynaptic endocytic zone membrane / dendritic spine head / D2 dopamine receptor binding / varicosity / postsynaptic neurotransmitter receptor internalization / membrane coat / G protein-coupled receptor internalization / positive regulation of synaptic vesicle endocytosis / clathrin-dependent endocytosis / endosome organization / photoreceptor ribbon synapse / response to amyloid-beta / regulation of synapse structure or activity / toxin transport / nitric-oxide synthase binding / photoreceptor inner segment / receptor internalization / synaptic vesicle / ephrin receptor signaling pathway / modulation of chemical synaptic transmission / postsynaptic membrane / SH3 domain binding / endocytosis / receptor-mediated endocytosis / cytoplasmic vesicle / microtubule / microtubule binding / protein C-terminus binding / dendritic spine / postsynaptic density / protein-containing complex binding / GTPase activity / synapse / myelin sheath / axon / glutamatergic synapse / GTP binding / protein kinase binding / Golgi apparatus / RNA binding / extracellular exosome / membrane / nucleoplasm / identical protein binding / plasma membrane / nucleus / cytoplasm / Dynamin-1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.75 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_citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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
P: Dynamin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,8096
Polyers171,7182
Non-polymers1,0914
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 17 / Rise per n subunits: 6.35 Å / Rotation per n subunits: 23.68 deg.

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Components

#1: Protein/peptide Dynamin-1 /


Mass: 85859.148 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1, DNM / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q05193, dynamin GTPase
#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Formula: C11H18N5O13P3 / Comment: GMP-PCP (energy-carrying molecule analogue) *YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium

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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: GMPPCP-bound Human Dynamin-1 helical polymer encasing a phosphatidylserine lipid membrane bilayer 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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 67 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 2.0.6 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 23.68 deg. / Axial rise/subunit: 6.35 Å / Axial symmetry: C1
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 452959 / Symmetry type: HELICAL

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