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Yorodumi- EMDB-10060: Cryo-EM structure of the human inner arm dynein DNAH7 microtubule... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10060 | |||||||||
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Title | Cryo-EM structure of the human inner arm dynein DNAH7 microtubule binding domain bound to microtubules | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | filament / complex / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information inner dynein arm / inner dynein arm assembly / axonemal dynein complex / COPI-independent Golgi-to-ER retrograde traffic / cilium-dependent cell motility / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cilium movement involved in cell motility / 9+2 motile cilium / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport ...inner dynein arm / inner dynein arm assembly / axonemal dynein complex / COPI-independent Golgi-to-ER retrograde traffic / cilium-dependent cell motility / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cilium movement involved in cell motility / 9+2 motile cilium / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Aggrephagy / positive regulation of intracellular transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cilium movement / regulation of metaphase plate congression / Resolution of Sister Chromatid Cohesion / establishment of spindle localization / positive regulation of spindle assembly / RHO GTPases Activate Formins / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / manchette / dynein complex / MHC class II antigen presentation / minus-end-directed microtubule motor activity / retrograde axonal transport / dynein light intermediate chain binding / cytoplasmic dynein complex / P-body assembly / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / nuclear migration / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / microtubule motor activity / dynein intermediate chain binding / cytoplasmic microtubule / cytoplasmic microtubule organization / stress granule assembly / regulation of mitotic spindle organization / axon cytoplasm / Neutrophil degranulation / mitotic spindle organization / filopodium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cilium / structural constituent of cytoskeleton / microtubule cytoskeleton organization / nuclear envelope / microtubule cytoskeleton / mitotic cell cycle / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / cell division / axon / GTPase activity / centrosome / neuronal cell body / calcium ion binding / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Lacey SE / He S | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Elife / Year: 2019 Title: Cryo-EM of dynein microtubule-binding domains shows how an axonemal dynein distorts the microtubule. Authors: Samuel E Lacey / Shaoda He / Sjors Hw Scheres / Andrew P Carter / Abstract: Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain ...Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain (MTBD) at the end of a coiled-coil stalk. We address how cytoplasmic and axonemal dynein MTBDs bind microtubules at near atomic resolution. We decorated microtubules with MTBDs of cytoplasmic dynein-1 and axonemal dynein DNAH7 and determined their cryo-EM structures using helical Relion. The majority of the MTBD is rigid upon binding, with the transition to the high-affinity state controlled by the movement of a single helix at the MTBD interface. DNAH7 contains an 18-residue insertion, found in many axonemal dyneins, that contacts the adjacent protofilament. Unexpectedly, we observe that DNAH7, but not dynein-1, induces large distortions in the microtubule cross-sectional curvature. This raises the possibility that dynein coordination in axonemes is mediated via conformational changes in the microtubule. | |||||||||
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_10060.map.gz | 69.2 MB | EMDB map data format | |
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Header (meta data) | emd-10060-v30.xml emd-10060.xml | 26.9 KB 26.9 KB | Display Display | EMDB header |
Images | emd_10060.png | 181.7 KB | ||
Masks | emd_10060_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-10060.cif.gz | 6.7 KB | ||
Others | emd_10060_additional.map.gz emd_10060_half_map_1.map.gz emd_10060_half_map_2.map.gz | 66.3 MB 411 MB 411 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10060 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10060 | HTTPS FTP |
-Validation report
Summary document | emd_10060_validation.pdf.gz | 1010.1 KB | Display | EMDB validaton report |
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Full document | emd_10060_full_validation.pdf.gz | 1009.7 KB | Display | |
Data in XML | emd_10060_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_10060_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10060 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10060 | HTTPS FTP |
-Related structure data
Related structure data | 6rzaMC 6rzbC 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_10060.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.085 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10060_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: None
File | emd_10060_additional.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Symmetrised half map
File | emd_10060_half_map_1.map | ||||||||||||
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Annotation | Symmetrised half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Symmetrised half map
File | emd_10060_half_map_2.map | ||||||||||||
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Annotation | Symmetrised half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : DNAH7 microtubule binding domain bound to microtubules
+Supramolecule #1: DNAH7 microtubule binding domain bound to microtubules
+Supramolecule #2: DNAH7
+Supramolecule #3: tubulin
+Macromolecule #1: Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain 7, axonemal...
+Macromolecule #2: Tubulin alpha-1B chain
+Macromolecule #3: Tubulin beta chain
+Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #5: MAGNESIUM ION
+Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #7: TAXOL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 67.5 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
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 41984 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-6rza: |