+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6701 | |||||||||
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Title | 3D cryo-EM reconstruction of Microtubule-WHAMM complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | microtubule / helical reconstruction / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information small GTPase binding => GO:0031267 / regulation of cell cycle => GO:0051726 / plasma membrane tubulation / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / positive regulation of actin nucleation / : / focal adhesion assembly / lamellipodium assembly / endoplasmic reticulum to Golgi vesicle-mediated transport ...small GTPase binding => GO:0031267 / regulation of cell cycle => GO:0051726 / plasma membrane tubulation / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / positive regulation of actin nucleation / : / focal adhesion assembly / lamellipodium assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / actin filament organization / cytoplasmic vesicle membrane / actin binding / microtubule binding / microtubule / Golgi membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Liu T / Wang HW | |||||||||
Citation | Journal: J Mol Biol / Year: 2017 Title: Structural Insights of WHAMM's Interaction with Microtubules by Cryo-EM. Authors: Tianyang Liu / Anbang Dai / Yong Cao / Rui Zhang / Meng-Qiu Dong / Hong-Wei Wang / Abstract: WASP homolog associated with actin, membranes, and microtubules (WHAMM) is a vertebrate protein functioning in membrane tubulation for intracellular membrane trafficking and specific organelle ...WASP homolog associated with actin, membranes, and microtubules (WHAMM) is a vertebrate protein functioning in membrane tubulation for intracellular membrane trafficking and specific organelle formation. Composed of multiple domains, WHAMM can bind to membrane and microtubule (MT) and promote actin polymerization nucleation. Previous work revealed that WHAMM's activity to promote actin nucleation is repressed upon binding to MTs. Here, we discovered that WHAMM interacts with αβ-tubulin through a small peptide motif within its MT-binding domain. We reconstructed a high-resolution structure of WHAMM's MT-binding motif (MBM) assembling around MTs using cryo-electron microscopy and verified it with chemical cross-linking and mass spectrometry analysis. We also detected a conformational switch of this motif between the non-MT-bound state and the MT-bound state. These discoveries provide new insights into the mechanism by which WHAMM coordinates actin and MT networks, the two major cytoskeletal systems involved in membrane trafficking and membrane remodeling. | |||||||||
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_6701.map.gz | 141.8 MB | EMDB map data format | |
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Header (meta data) | emd-6701-v30.xml emd-6701.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | emd_6701.png | 298.9 KB | ||
Filedesc metadata | emd-6701.cif.gz | 4.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6701 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6701 | HTTPS FTP |
-Validation report
Summary document | emd_6701_validation.pdf.gz | 501.7 KB | Display | EMDB validaton report |
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Full document | emd_6701_full_validation.pdf.gz | 501.3 KB | Display | |
Data in XML | emd_6701_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | emd_6701_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6701 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6701 | HTTPS FTP |
-Related structure data
Related structure data | 5x1gMC 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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-Map
File | Download / File: emd_6701.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.306 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 : Ternary complex of alpha,beta-tubulin dimer with microtubule bind...
Entire | Name: Ternary complex of alpha,beta-tubulin dimer with microtubule binding motif of WHAMM |
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Components |
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-Supramolecule #1: Ternary complex of alpha,beta-tubulin dimer with microtubule bind...
Supramolecule | Name: Ternary complex of alpha,beta-tubulin dimer with microtubule binding motif of WHAMM type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: WASP homolog-associated protein with actin, membranes and microtubules
Macromolecule | Name: WASP homolog-associated protein with actin, membranes and microtubules type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 4.414182 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: IQMKRDKIKE EEQKKKEWIN QERQKTLQRL RSFK UniProtKB: WASP homolog-associated protein with actin, membranes and microtubules |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 8.6 Å Applied symmetry - Helical parameters - Δ&Phi: -25.762 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8000 |
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Startup model | Type of model: OTHER |
Final angle assignment | Type: NOT APPLICABLE |