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- PDB-4uuk: Human dynamin 1 K44A superconstricted polymer stabilized with GTP... -

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Basic information

Entry
Database: PDB / ID: 4uuk
TitleHuman dynamin 1 K44A superconstricted polymer stabilized with GTP strand 2
Components(DYNAMIN-1) x 2
KeywordsHYDROLASE / DYNAMIN / ENDOCYTOSIS / MEMBRANE FISSION / GTPASE / INTRACELLULAR TRAFFICKING
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
Biological speciesHOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsSundborger, A.C. / Fang, S. / Heymann, J.A. / Ray, P. / Chappie, J.S. / Hinshaw, J.E.
CitationJournal: Cell Rep / Year: 2014
Title: A dynamin mutant defines a superconstricted prefission state.
Authors: Anna C Sundborger / Shunming Fang / Jürgen A Heymann / Pampa Ray / Joshua S Chappie / Jenny E Hinshaw /
Abstract: Dynamin is a 100 kDa GTPase that organizes into helical assemblies at the base of nascent clathrin-coated vesicles. Formation of these oligomers stimulates the intrinsic GTPase activity of dynamin, ...Dynamin is a 100 kDa GTPase that organizes into helical assemblies at the base of nascent clathrin-coated vesicles. Formation of these oligomers stimulates the intrinsic GTPase activity of dynamin, which is necessary for efficient membrane fission during endocytosis. Recent evidence suggests that the transition state of dynamin's GTP hydrolysis reaction serves as a key determinant of productive fission. Here, we present the structure of a transition-state-defective dynamin mutant K44A trapped in a prefission state at 12.5 Å resolution. This structure constricts to 3.7 nm, reaching the theoretical limit required for spontaneous membrane fission. Computational docking indicates that the ground-state conformation of the dynamin polymer is sufficient to achieve this superconstricted prefission state and reveals how a two-start helical symmetry promotes the most efficient packing of dynamin tetramers around the membrane neck. These data suggest a model for the assembly and regulation of the minimal dynamin fission machine.
History
DepositionJul 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: em_image_scans / em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: DYNAMIN-1
B: DYNAMIN-1
C: DYNAMIN-1
D: DYNAMIN-1
E: DYNAMIN-1
F: DYNAMIN-1
G: DYNAMIN-1
H: DYNAMIN-1
I: DYNAMIN-1
J: DYNAMIN-1
K: DYNAMIN-1
L: DYNAMIN-1


Theoretical massNumber of molelcules
Total (without water)1,170,44412
Polymers1,170,44412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
DYNAMIN-1 / HUMAN DYNAMIN 1


Mass: 97536.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMALC2XP5D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05193, dynamin GTPase
#2: Protein
DYNAMIN-1 / HUMAN DYNAMIN 1


Mass: 97537.344 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q05193, dynamin GTPase

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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: GTP STABILIZED HUMAN DYNAMIN 1 K44A SUPER CONSTRICTED POLYMER
Type: COMPLEX
Details: K44A DYNAMIN HELICAL TUBES GENERATED IN THE PRESENCE OF GTP AND DOPS LIPOSOMES
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Details: PLUNGE FROZEN IN LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/HE / Date: Dec 17, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 49000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Yup.scxmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: INDIVIDUAL IMAGES
3D reconstructionMethod: IHRSR / Resolution: 12.5 Å / Num. of particles: 7525 / Nominal pixel size: 2.55 Å
Details: THIS MODEL INCORPORATES COORDINATES FROM 3ZYC, , 3SNH, AND 1DYN, WHICH WERE DOCKED INTO A HELICAL CRYO-EM DENSITY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-270. COORDINATES HERE ...Details: THIS MODEL INCORPORATES COORDINATES FROM 3ZYC, , 3SNH, AND 1DYN, WHICH WERE DOCKED INTO A HELICAL CRYO-EM DENSITY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-270. COORDINATES HERE REPRESENT STRAND 2 OF THE TWO- -START HELIX
Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--YUP ALGORITHM REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13ZYC

3zyc

13ZYC1PDBexperimental model
23SNH

3snh

13SNH2PDBexperimental model
31DYN

1dyn

11DYN3PDBexperimental model
RefinementHighest resolution: 12.5 Å
Refinement stepCycle: LAST / Highest resolution: 12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21116 0 0 0 21116

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