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Yorodumi- EMDB-6049: Cryo-EM structure of the yeast dynein motor domain in the presenc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6049 | |||||||||
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Title | Cryo-EM structure of the yeast dynein motor domain in the presence of ADP-vanadate | |||||||||
Map data | Reconstruction of yeast dynein motor domain in the presence of 5 mM ADP-vanadate (prepared by mixing ATP and vanadate in equimolar amounts) | |||||||||
Sample |
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Keywords | motor proteins / power stroke / dynein / AAA protein / ATPase | |||||||||
Function / homology | Function and homology information karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / spindle pole body / dynein intermediate chain binding ...karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / spindle pole body / dynein intermediate chain binding / cytoplasmic microtubule / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / cell cortex / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 Å | |||||||||
Authors | Bhabha G / Moeller A / Liao M / Speir JA / Vale RD / Cheng Y | |||||||||
Citation | Journal: Cell / Year: 2014 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6049.map.gz | 2.9 MB | EMDB map data format | |
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Header (meta data) | emd-6049-v30.xml emd-6049.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | emd_6049.png | 213.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6049 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6049 | HTTPS FTP |
-Validation report
Summary document | emd_6049_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_6049_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_6049_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6049 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6049 | HTTPS FTP |
-Related structure data
Related structure data | 6047C 6048C 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 (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_6049.map.gz / Format: CCP4 / Size: 3.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of yeast dynein motor domain in the presence of 5 mM ADP-vanadate (prepared by mixing ATP and vanadate in equimolar amounts) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.43 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 : yeast dynein motor domain in the presence of ADP-vanadate
Entire | Name: yeast dynein motor domain in the presence of ADP-vanadate |
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Components |
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-Supramolecule #1000: yeast dynein motor domain in the presence of ADP-vanadate
Supramolecule | Name: yeast dynein motor domain in the presence of ADP-vanadate 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: Saccharomyces cerevisiae (brewer's yeast) / Strain: VY1027 / synonym: yeast |
Molecular weight | Theoretical: 303 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | UniProtKB: Dynein heavy chain, cytoplasmic |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Details | Gatan K2 Summit operated in super-resolution counting mode; image recorded with dose fractionation method. |
Date | Nov 3, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 657 / Average electron dose: 21 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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: 31000 |
Sample stage | Specimen holder: cooled to liquid nitrogen temperature / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each particle |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 8042 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |