[English] 日本語
Yorodumi- PDB-7mi8: Signal subtracted reconstruction of AAA5 and AAA6 domains of dyne... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mi8 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Signal subtracted reconstruction of AAA5 and AAA6 domains of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Model 5 | |||||||||||||||
Components | Fusion protein of Dynein and Endolysin | |||||||||||||||
Keywords | MOTOR PROTEIN / AAA ATPase / ATPase inhibitor | |||||||||||||||
Function / homology | Function and homology information karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / nuclear migration / spindle pole body / dynein intermediate chain binding ...karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
Authors | Santarossa, C.C. / Coudray, N. / Urnavicius, L. / Ekiert, D.C. / Bhabha, G. / Kapoor, T.M. | |||||||||||||||
Funding support | United States, 4items
| |||||||||||||||
Citation | Journal: Cell Chem Biol / Year: 2021 Title: Targeting allostery in the Dynein motor domain with small molecule inhibitors. Authors: Cristina C Santarossa / Keith J Mickolajczyk / Jonathan B Steinman / Linas Urnavicius / Nan Chen / Yasuhiro Hirata / Yoshiyuki Fukase / Nicolas Coudray / Damian C Ekiert / Gira Bhabha / Tarun M Kapoor / Abstract: Cytoplasmic dyneins are AAA (ATPase associated with diverse cellular activities) motor proteins responsible for microtubule minus-end-directed intracellular transport. Dynein's unusually large size, ...Cytoplasmic dyneins are AAA (ATPase associated with diverse cellular activities) motor proteins responsible for microtubule minus-end-directed intracellular transport. Dynein's unusually large size, four distinct nucleotide-binding sites, and conformational dynamics pose challenges for the design of potent and selective chemical inhibitors. Here we use structural approaches to develop a model for the inhibition of a well-characterized S. cerevisiae dynein construct by pyrazolo-pyrimidinone-based compounds. These data, along with functional assays of dynein motility and mutagenesis studies, suggest that the compounds inhibit dynein by engaging the regulatory ATPase sites in the AAA3 and AAA4 domains, and not by interacting with dynein's main catalytic site in the AAA1 domain. A double Walker B mutation of the AAA3 and AAA4 sites substantially reduces enzyme activity, suggesting that targeting these regulatory domains is sufficient to inhibit dynein. Our findings reveal how chemical inhibitors can be designed to disrupt allosteric communication across dynein's AAA domains. | |||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7mi8.cif.gz | 266.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7mi8.ent.gz | 175.2 KB | Display | PDB format |
PDBx/mmJSON format | 7mi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mi8_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7mi8_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7mi8_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 7mi8_validation.cif.gz | 52.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/7mi8 ftp://data.pdbj.org/pub/pdb/validation_reports/mi/7mi8 | HTTPS FTP |
-Related structure data
Related structure data | 23842MC 7mi1C 7mi3C 7mi6C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 304889.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Enterobacteria phage T4 (virus) Gene: DYN1, DHC1, YKR054C / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): VY972 / References: UniProt: P36022, UniProt: P00720 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Dynein motor domain in the presence of a pyrazolo-pyrimidinone-based compound Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.3 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||||||||||||
Source (natural) |
| |||||||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: VY972 | |||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1300 nm / Calibrated defocus max: 3700 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 10 sec. / Electron dose: 44 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4893 |
Image scans | Width: 7420 / Height: 7676 / Movie frames/image: 50 |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128004 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7MI1 Pdb chain-ID: A / Accession code: 7MI1 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|