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Open data
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Basic information
Entry | Database: PDB / ID: 3zys | ||||||
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Title | Human dynamin 1 deltaPRD polymer stabilized with GMPPCP | ||||||
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![]() | HYDROLASE/GTP-BINDING PROTEIN / HYDROLASE-GTP-BINDING PROTEIN COMPLEX / ENDOCYTOSIS / GTP HYDROLYSIS / MEMBRANE REMODELING | ||||||
Function / homology | ![]() clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / interleukin-27-mediated signaling pathway / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / interleukin-27-mediated signaling pathway / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Formation of annular gap junctions / endosome organization / Gap junction degradation / photoreceptor ribbon synapse / membrane coat / response to type I interferon / negative regulation of viral genome replication / Recycling pathway of L1 / phosphatidylinositol-3,4,5-trisphosphate binding / antiviral innate immune response / endocytic vesicle / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / photoreceptor inner segment / receptor-mediated endocytosis / cell projection / response to virus / modulation of chemical synaptic transmission / protein homooligomerization / receptor internalization / ISG15 antiviral mechanism / defense response / endocytosis / GDP binding / : / Interferon alpha/beta signaling / presynapse / Clathrin-mediated endocytosis / microtubule binding / nuclear membrane / protein homotetramerization / defense response to virus / microtubule / innate immune response / GTPase activity / glutamatergic synapse / apoptotic process / synapse / endoplasmic reticulum membrane / GTP binding / protein kinase binding / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 12.2 Å | ||||||
![]() | Chappie, J.S. / Mears, J.A. / Fang, S. / Leonard, M. / Schmid, S.L. / Milligan, R.A. / Hinshaw, J.E. / Dyda, F. | ||||||
![]() | ![]() Title: A pseudoatomic model of the dynamin polymer identifies a hydrolysis-dependent powerstroke. Authors: Joshua S Chappie / Jason A Mears / Shunming Fang / Marilyn Leonard / Sandra L Schmid / Ronald A Milligan / Jenny E Hinshaw / Fred Dyda / ![]() Abstract: The GTPase dynamin catalyzes membrane fission by forming a collar around the necks of clathrin-coated pits, but the specific structural interactions and conformational changes that drive this process ...The GTPase dynamin catalyzes membrane fission by forming a collar around the necks of clathrin-coated pits, but the specific structural interactions and conformational changes that drive this process remain a mystery. We present the GMPPCP-bound structures of the truncated human dynamin 1 helical polymer at 12.2 Å and a fusion protein, GG, linking human dynamin 1's catalytic G domain to its GTPase effector domain (GED) at 2.2 Å. The structures reveal the position and connectivity of dynamin fragments in the assembled structure, showing that G domain dimers only form between tetramers in sequential rungs of the dynamin helix. Using chemical crosslinking, we demonstrate that dynamin tetramers are made of two dimers, in which the G domain of one molecule interacts in trans with the GED of another. Structural comparison of GG(GMPPCP) to the GG transition-state complex identifies a hydrolysis-dependent powerstroke that may play a role in membrane-remodeling events necessary for fission. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260.3 KB | Display | ![]() |
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PDB format | ![]() | 191.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 935.9 KB | Display | ![]() |
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Full document | ![]() | 1002 KB | Display | |
Data in XML | ![]() | 47.9 KB | Display | |
Data in CIF | ![]() | 70 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1949MC ![]() 3zycC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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3 | ![]()
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 12 / Rise per n subunits: 15.045 Å / Rotation per n subunits: 54.545 °) |
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Components
#1: Protein | Mass: 39388.961 Da / Num. of mol.: 2 Fragment: G DOMAIN, RESIDUES 1-320, GTPASE EFFECTOR DOMAIN, RESIDUES 726-750 Source method: isolated from a genetically manipulated source Details: EIGHT AMINO ACID POLYPEPTIDE LINKER BETWEEN G DOMAIN AND GTPASE EFFECTOR DOMAIN, RESIDUES 321-328 Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 75623.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 13440.362 Da / Num. of mol.: 2 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 518-630 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: GMPPCP STABILIZED HUMAN DYNAMIN 1 DELTA PRD HELICAL POLYMER Type: COMPLEX Details: DELTA PRD DYNAMIN HELICAL TUBES GENERATED IN THE PRESENCE OF GMPPCP AND DOPS LIPOSOMES |
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Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: PLUNGE FROZEN IN LIQUID ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: INDIVIDUAL IMAGES USING ACE2 | ||||||||||||||||||||||||||||
3D reconstruction | Method: IHRSR / Resolution: 12.2 Å / Num. of particles: 4814 / Nominal pixel size: 2.26 Å Details: THIS MODEL INCORPORATES COORDINATES FROM 3ZYC AND 1DYN, WHICH WERE DOCKED INTO A HELICAL CRYO-EM DENSITY. CHAINS A AND D OF THE MODEL SHOW RESIDUES 6-311 OF HUMAN DYNAMIN 1'S G DOMAIN AND ...Details: THIS MODEL INCORPORATES COORDINATES FROM 3ZYC AND 1DYN, WHICH WERE DOCKED INTO A HELICAL CRYO-EM DENSITY. CHAINS A AND D OF THE MODEL SHOW RESIDUES 6-311 OF HUMAN DYNAMIN 1'S G DOMAIN AND RESIDUES 726-748 OF ITS GTPASE EFFECTOR DOMAIN. CHAINS C AND F INCLUDE RESIDUES 518-630 OF DYNAMIN'S PH DOMAIN. RESIDUE 5 SER IN CHAINS A AND D IS A CLONING ARTIFACT THAT WAS VISIBLE IN THE CRYSTAL STRUCTURE OF 3ZYC. INCORPORATES COORDINATES FROM 3LJB, WHICH WERE DOCKED INTO A HELICAL CRYO-EM DENSITY. CHAINS B AND E INCLUDE RESIDUES 367-435 AND 451-531 OF HUMAN MXA'S MIDDLE DOMAIN AND RESIDUES 576-636 OF IF GTPASE EFFECTOR DOMAIN. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1949. (DEPOSITION ID: 10194). Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Details: REFINEMENT PROTOCOL--YUP ALGORITHM | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 12.2 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 12.2 Å
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