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- PDB-8t0k: Cryo-EM of the GDP-bound human dynamin (full-length) polymer asse... -

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Basic information

Entry
Database: PDB / ID: 8t0k
TitleCryo-EM of the GDP-bound human dynamin (full-length) polymer assembled on the membrane in the super constricted state
ComponentsDynamin-1
KeywordsHYDROLASE / dynamin / membrane / fission / lipid / tubule / scission / endocytosis
Function / homology
Function and homology information


clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Retrograde neurotrophin signalling / Toll Like Receptor 4 (TLR4) Cascade / Formation of annular gap junctions / endosome organization ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / Retrograde neurotrophin signalling / Toll Like Receptor 4 (TLR4) Cascade / Formation of annular gap junctions / endosome organization / Gap junction degradation / phosphatidylinositol-3,4,5-trisphosphate binding / Recycling pathway of L1 / EPH-ephrin mediated repulsion of cells / endocytic vesicle / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / receptor-mediated endocytosis / cell projection / protein homooligomerization / receptor internalization / endocytosis / GDP binding / presynapse / Clathrin-mediated endocytosis / protein homotetramerization / microtubule binding / microtubule / GTPase activity / synapse / protein kinase binding / GTP binding / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Dynamin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsJimah, J.R. / Canagarajah, B.J. / Hinshaw, J.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIADK060100 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM140220 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM140220 United States
CitationJournal: Dev Cell / Year: 2024
Title: Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission.
Authors: John R Jimah / Nidhi Kundu / Abigail E Stanton / Kem A Sochacki / Bertram Canagarajah / Lieza Chan / Marie-Paule Strub / Huaibin Wang / Justin W Taraska / Jenny E Hinshaw /
Abstract: Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the ...Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the plasma membrane. Although atomic models of the dynamin helical polymer bound to guanosine triphosphate (GTP) analogs define earlier stages of membrane constriction, there are no atomic models of the assembled state post-GTP hydrolysis. Here, we used cryo-EM methods to determine atomic structures of the dynamin helical polymer assembled on lipid tubules, akin to necks of budding endocytic vesicles, in a guanosine diphosphate (GDP)-bound, super-constricted state. In this state, dynamin is assembled as a 2-start helix with an inner lumen of 3.4 nm, primed for spontaneous fission. Additionally, by cryo-electron tomography, we trapped dynamin helical assemblies within HeLa cells using the GTPase-defective dynamin K44A mutant and observed diverse dynamin helices, demonstrating that dynamin can accommodate a range of assembled complexes in cells that likely precede membrane fission.
History
DepositionJun 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
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Revision 1.1May 8, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)397,17312
Polymers395,3034
Non-polymers1,8708
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Dynamin-1


Mass: 98825.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1, DNM / Production host: Homo sapiens (human) / References: UniProt: Q05193, dynamin GTPase
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: GDP-bound human dynamin (full-length) helical polymer assembled on the membrane
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 98.7 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 26.155 ° / Axial rise/subunit: 14.673 Å / Axial symmetry: C1
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 626859 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00722906
ELECTRON MICROSCOPYf_angle_d0.7930888
ELECTRON MICROSCOPYf_dihedral_angle_d10.368852
ELECTRON MICROSCOPYf_chiral_restr0.0483470
ELECTRON MICROSCOPYf_plane_restr0.0043998

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