+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1949 | |||||||||
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Title | Human dynamin 1 deltaPRD polymer stabilized with GMPPCP | |||||||||
Map data | Three-dimensional volume of deltaPRD human dynamin 1 polymer | |||||||||
Sample |
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Keywords | dynamin / endocytosis / GTP hydrolysis / membrane remodeling | |||||||||
Function / homology | Function and homology information 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 / endosome organization / Formation of annular gap junctions / photoreceptor ribbon synapse / Gap junction degradation / membrane coat / response to type I interferon / negative regulation of viral genome replication / Recycling pathway of L1 / phosphatidylinositol-3,4,5-trisphosphate binding / endocytic vesicle / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / antiviral innate immune response / 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 / Clathrin-mediated endocytosis / presynapse / nuclear membrane / microtubule binding / protein homotetramerization / defense response to virus / microtubule / innate immune response / GTPase activity / glutamatergic synapse / synapse / endoplasmic reticulum membrane / GTP binding / protein kinase binding / apoptotic process / 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 | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 12.2 Å | |||||||||
Authors | Chappie JS / Mears JA / Fang S / Leonard M / Schmid SL / Milligan RA / Hinshaw JE / Dyda F | |||||||||
Citation | Journal: Cell / Year: 2011 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1949.map.gz | 7.2 MB | EMDB map data format | |
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Header (meta data) | emd-1949-v30.xml emd-1949.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_1949.tif | 360.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1949 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1949 | HTTPS FTP |
-Related structure data
Related structure data | 3zysMC 3zycC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1949.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Three-dimensional volume of deltaPRD human dynamin 1 polymer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : GMPPCP-stablized human dynamin 1 delta PRD polymer
Entire | Name: GMPPCP-stablized human dynamin 1 delta PRD polymer |
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Components |
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-Supramolecule #1000: GMPPCP-stablized human dynamin 1 delta PRD polymer
Supramolecule | Name: GMPPCP-stablized human dynamin 1 delta PRD polymer / type: sample / ID: 1000 / Oligomeric state: Helical assembly of dynamin tetramers / Number unique components: 3 |
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-Macromolecule #1: Human dynamin 1 delta PRD
Macromolecule | Name: Human dynamin 1 delta PRD / type: protein_or_peptide / ID: 1 / Name.synonym: Human dynamin 1 delta PRD / Details: contains bound GMPPCP / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane and cytosol |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: PMALC2XP5D |
-Macromolecule #2: Human dynamin 1 pleckstrin homology domain
Macromolecule | Name: Human dynamin 1 pleckstrin homology domain / type: protein_or_peptide / ID: 2 / Name.synonym: Human dynamin 1 pleckstrin homology domain / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane and cytosol |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: PSKB-LNB |
-Macromolecule #3: Interferon-induced GTP-binding protein Mx1
Macromolecule | Name: Interferon-induced GTP-binding protein Mx1 / type: protein_or_peptide / ID: 3 / Name.synonym: Interferon-induced GTP-binding protein Mx1 / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: PET11A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 Details: 20 mM Hepes pH 7.5, 50 mM NaCl, 2 mM EGTA, 4 mM MgCl2, 1 mM DTT, 1 mg/ml 0.4 um 1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPS) liposomes, 2 mM GMPPCP |
Grid | Details: 400 mesh C-flat grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Manual Method: Absorbed samples to grids, blotted, washed with 20 mM Hepes pH 7.5, blotted and plunged. |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Temperature | Min: 93 K / Max: 95 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000X magnification |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 10 e/Å2 / Details: Images were collected on CCD |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Gatan 626 side entry cryo-stage / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 7.52 Å Applied symmetry - Helical parameters - Δ&Phi: 27.3 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider Details: A total of 4,814 helical segments were incorporated by the IHRSR algorithm into the final reconstruction after 50 cycles |
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CTF correction | Details: Each image using ACE2 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: YUP |
Details | PDBEntryID_givenInChain. Protocol: Manual and Flexible fitting. Models were initially placed manually and initial positions were refined using the YUP.SCX method of the YUP software package |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-3zys: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: YUP |
Details | PDBEntryID_givenInChain. Protocol: Manual and Flexible fitting. Models were initially placed manually and initial positions were refined using the YUP.SCX method of the YUP software package |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-3zys: |
-Atomic model buiding 3
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: YUP |
Details | PDBEntryID_givenInChain. Protocol: Manual and Flexible fitting. Models were initially placed manually and initial positions were refined using the YUP.SCX method of the YUP software package |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-3zys: |