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Yorodumi- EMDB-2157: Helical structures of WHAMM around MTs revealed by Electron cryo-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2157 | |||||||||
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Title | Helical structures of WHAMM around MTs revealed by Electron cryo-microscopy | |||||||||
Map data | Reconstruction of WHAMM with N-terminal MBP | |||||||||
Sample |
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Keywords | actin nucleation / membrane tubulation / microtubules / WHAMM | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 18.0 Å | |||||||||
Authors | Shen QT / Hsiue PP / Sindelar CV / Welch MD / Campellone KG / Wang HW | |||||||||
Citation | Journal: J Cell Biol / Year: 2012 Title: Structural insights into WHAMM-mediated cytoskeletal coordination during membrane remodeling. Authors: Qing-Tao Shen / Peter P Hsiue / Charles V Sindelar / Matthew D Welch / Kenneth G Campellone / Hong-Wei Wang / Abstract: The microtubule (MT) and actin cytoskeletons drive many essential cellular processes, yet fairly little is known about how their functions are coordinated. One factor that mediates important cross ...The microtubule (MT) and actin cytoskeletons drive many essential cellular processes, yet fairly little is known about how their functions are coordinated. One factor that mediates important cross talk between these two systems is WHAMM, a Golgi-associated protein that utilizes MT binding and actin nucleation activities to promote membrane tubulation during intracellular transport. Using cryoelectron microscopy and other biophysical and biochemical approaches, we unveil the underlying mechanisms for how these activities are coordinated. We find that WHAMM bound to the outer surface of MT protofilaments via a novel interaction between its central coiled-coil region and tubulin heterodimers. Upon the assembly of WHAMM onto MTs, its N-terminal membrane-binding domain was exposed at the MT periphery, where it can recruit vesicles and remodel them into tubular structures. In contrast, MT binding masked the C-terminal portion of WHAMM and prevented it from promoting actin nucleation. These results give rise to a model whereby distinct MT-bound and actin-nucleating populations of WHAMM collaborate during membrane tubulation. | |||||||||
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_2157.map.gz | 26.6 MB | EMDB map data format | |
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Header (meta data) | emd-2157-v30.xml emd-2157.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | EMD-2157.png | 178.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2157 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2157 | HTTPS FTP |
-Validation report
Summary document | emd_2157_validation.pdf.gz | 260.1 KB | Display | EMDB validaton report |
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Full document | emd_2157_full_validation.pdf.gz | 259.3 KB | Display | |
Data in XML | emd_2157_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2157 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2157 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2157.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of WHAMM with N-terminal MBP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.7 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 : WHAMM around 13-pf MTs
Entire | Name: WHAMM around 13-pf MTs |
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Components |
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-Supramolecule #1000: WHAMM around 13-pf MTs
Supramolecule | Name: WHAMM around 13-pf MTs / type: sample / ID: 1000 / Number unique components: 117 |
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-Macromolecule #1: WHAMM around MTs
Macromolecule | Name: WHAMM around MTs / type: protein_or_peptide / ID: 1 / Number of copies: 17 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / Strain: Hela / synonym: Human |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 / Details: 80mM PIPES pH 6.8, 1mM MgCl2, 1mM EGTA, 1mM DTT |
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Grid | Details: 300 mesh holly carbon grid, glow discharged. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 2.5 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 88 K / Max: 101 K / Average: 95 K |
Date | Nov 16, 2009 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 77 / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 34000 / Illumination mode: OTHER / Imaging mode: DIFFRACTION / Cs: 2.2 mm / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.0015 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: OTHER / Software - Name: Spider, EMAN |
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CTF correction | Details: Each particle |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: Chimera |
Details | Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |