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Yorodumi- PDB-4w8f: Crystal structure of the dynein motor domain in the AMPPNP-bound state -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w8f | ||||||
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Title | Crystal structure of the dynein motor domain in the AMPPNP-bound state | ||||||
Components | Dynein heavy chain lysozyme chimera | ||||||
Keywords | MOTOR PROTEIN / cytoplasmic dynein / microtubule / ATPase / AAA+ / AMPPNP | ||||||
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 / viral release from host cell by cytolysis / Neutrophil degranulation / peptidoglycan catabolic process / mitotic spindle organization / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / cell cortex / host cell cytoplasm / defense response to bacterium / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.541 Å | ||||||
Authors | Cheng, H.-C. / Bhabha, G. / Zhang, N. / Vale, R.D. | ||||||
Funding support | United States, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w8f.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4w8f.ent.gz | 2.5 MB | Display | PDB format |
PDBx/mmJSON format | 4w8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w8f_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 4w8f_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 4w8f_validation.xml.gz | 174 KB | Display | |
Data in CIF | 4w8f_validation.cif.gz | 233.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/4w8f ftp://data.pdbj.org/pub/pdb/validation_reports/w8/4w8f | HTTPS FTP |
-Related structure data
Related structure data | 6047C 6048C 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 C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 304889.875 Da / Num. of mol.: 2 / Mutation: E1849Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Enterobacteria phage T4 (virus) Strain: ATCC 204508 / S288c / Gene: DYN1, DHC1, YKR054C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36022, UniProt: P00720, lysozyme #2: Chemical | ChemComp-ANP / #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.7 % / Description: thin plates |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 4-10% PEG 3350 and 200-300 mM NaAc |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 3.54→49.4 Å / Num. obs: 82983 / % possible obs: 92.2 % / Observed criterion σ(I): 3.3 / Redundancy: 10.9 % / Net I/σ(I): 8.9 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_1769) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3.541→49.4 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.541→49.4 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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