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- EMDB-6048: Cryo-EM structure of the dynein motor domain in the presence of A... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6048 | |||||||||
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Title | Cryo-EM structure of the dynein motor domain in the presence of ADP-AlF3 | |||||||||
![]() | Reconstruction of dynein motor domain in the presence of ADP-AlF3 (class2) | |||||||||
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![]() | motor proteins / power stroke / dynein / AAA protein / ATPase | |||||||||
Function / homology | ![]() karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / spindle pole body / cytoplasmic dynein complex / retrograde axonal transport / nuclear migration ...karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / spindle pole body / cytoplasmic dynein complex / retrograde axonal transport / nuclear migration / dynein intermediate chain binding / cytoplasmic microtubule / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / cell cortex / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.0 Å | |||||||||
![]() | Bhabha G / Moeller A / Liao M / Speir JA / Vale RD / Cheng Y | |||||||||
![]() | ![]() Title: Allosteric communication in the dynein motor domain. Authors: Gira Bhabha / Hui-Chun Cheng / Nan Zhang / Arne Moeller / Maofu Liao / Jeffrey A Speir / Yifan Cheng / Ronald D Vale / ![]() Abstract: Dyneins power microtubule motility using ring-shaped, AAA-containing motor domains. Here, we report X-ray and electron microscopy (EM) structures of yeast dynein bound to different ATP analogs, which ...Dyneins power microtubule motility using ring-shaped, AAA-containing motor domains. Here, we report X-ray and electron microscopy (EM) structures of yeast dynein bound to different ATP analogs, which collectively provide insight into the roles of dynein's two major ATPase sites, AAA1 and AAA3, in the conformational change mechanism. ATP binding to AAA1 triggers a cascade of conformational changes that propagate to all six AAA domains and cause a large movement of the "linker," dynein's mechanical element. In contrast to the role of AAA1 in driving motility, nucleotide transitions in AAA3 gate the transmission of conformational changes between AAA1 and the linker, suggesting that AAA3 acts as a regulatory switch. Further structural and mutational studies also uncover a role for the linker in regulating the catalytic cycle of AAA1. Together, these results reveal how dynein's two major ATP-binding sites initiate and modulate conformational changes in the motor domain during motility. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 758.3 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.8 KB 9.8 KB | Display Display | ![]() |
Images | ![]() | 116.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.4 KB | Display | ![]() |
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Full document | ![]() | 77.5 KB | Display | |
Data in XML | ![]() | 495 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6047C ![]() 6049C ![]() 6050C ![]() 6051C ![]() 6052C ![]() 6053C ![]() 6054C ![]() 6055C ![]() 6056C ![]() 6058C ![]() 6059C ![]() 6060C ![]() 6061C ![]() 6062C ![]() 6063C ![]() 6064C ![]() 6065C ![]() 6066C ![]() 6067C ![]() 6068C ![]() 6069C ![]() 6070C ![]() 6071C ![]() 6072C ![]() 6073C ![]() 6074C ![]() 4w8fC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of dynein motor domain in the presence of ADP-AlF3 (class2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.78 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : yeast dynein motor domain bound to ADP-AlF3 (class 2)
Entire | Name: yeast dynein motor domain bound to ADP-AlF3 (class 2) |
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Components |
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-Supramolecule #1000: yeast dynein motor domain bound to ADP-AlF3 (class 2)
Supramolecule | Name: yeast dynein motor domain bound to ADP-AlF3 (class 2) / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 303 KDa |
-Macromolecule #1: dynein
Macromolecule | Name: dynein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 303 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Dynein heavy chain, cytoplasmic |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 8 Details: 50 mM Tris, pH 8.0, 200 mM sodium chloride, 1 mM EGTA, 2 mM magnesium acetate, 1 mM DTT |
Grid | Details: Quantifoil, Cu 400 mesh, R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK II / Method: blot for 4 seconds before plunging |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Nov 6, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 1001 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: each particle |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 44829 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: ![]() |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |