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Yorodumi- PDB-5vh9: Cryo-EM structure of yeast cytoplasmic dynein-1 with Lis1 and ATP -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vh9 | |||||||||
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Title | Cryo-EM structure of yeast cytoplasmic dynein-1 with Lis1 and ATP | |||||||||
Components |
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Keywords | MOTOR PROTEIN / cytoplasmic dynein / lis1 | |||||||||
Function / homology | Function and homology information microtubule sliding / 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 / microtubule associated complex ...microtubule sliding / 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 / microtubule associated complex / spindle pole body / dynein intermediate chain binding / dynein complex binding / cytoplasmic microtubule / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / spindle pole / cell cortex / microtubule / cell division / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.7 Å | |||||||||
Authors | Cianfrocco, M.A. / DeSantis, M.E. / Htet, Z.M. / Tran, P.T. / Reck-Peterson, S.L. / Leschziner, A.E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell / Year: 2017 Title: Lis1 Has Two Opposing Modes of Regulating Cytoplasmic Dynein. Authors: Morgan E DeSantis / Michael A Cianfrocco / Zaw Min Htet / Phuoc Tien Tran / Samara L Reck-Peterson / Andres E Leschziner / Abstract: Regulation is central to the functional versatility of cytoplasmic dynein, a motor involved in intracellular transport, cell division, and neurodevelopment. Previous work established that Lis1, a ...Regulation is central to the functional versatility of cytoplasmic dynein, a motor involved in intracellular transport, cell division, and neurodevelopment. Previous work established that Lis1, a conserved regulator of dynein, binds to its motor domain and induces a tight microtubule-binding state in dynein. The work we present here-a combination of biochemistry, single-molecule assays, and cryoelectron microscopy-led to the surprising discovery that Lis1 has two opposing modes of regulating dynein, being capable of inducing both low and high affinity for the microtubule. We show that these opposing modes depend on the stoichiometry of Lis1 binding to dynein and that this stoichiometry is regulated by the nucleotide state of dynein's AAA3 domain. The low-affinity state requires Lis1 to also bind to dynein at a novel conserved site, mutation of which disrupts Lis1's function in vivo. We propose a new model for the regulation of dynein by Lis1. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5vh9.cif.gz | 850.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vh9.ent.gz | 706.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vh9_validation.pdf.gz | 660.8 KB | Display | wwPDB validaton report |
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Full document | 5vh9_full_validation.pdf.gz | 702.5 KB | Display | |
Data in XML | 5vh9_validation.xml.gz | 73.3 KB | Display | |
Data in CIF | 5vh9_validation.cif.gz | 112.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/5vh9 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/5vh9 | HTTPS FTP |
-Related structure data
Related structure data | 8673MC 8706C 5vljC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 272666.250 Da / Num. of mol.: 1 / Fragment: UNP residues 1448-3028,3298-4092 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DYN1, DHC1, YKR054C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36022 |
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#2: Protein | Mass: 40645.449 Da / Num. of mol.: 1 / Fragment: UNP residues 140-493 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PAC1, LIS1, SCY_5321 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A6ZPA6 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Dynein-Lis1 co-complex with ATP / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.444 MDa / Experimental value: YES |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Plasmid: RPY1302 |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.23 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: No pretreatment of grids / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil UltrAuFoil 1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 276 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Calibrated defocus min: 2000 nm / Calibrated defocus max: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.15 sec. / Electron dose: 82 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 5614 |
Image scans | Movie frames/image: 53 / Used frames/image: 3-53 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
3D reconstruction | Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25520 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | B value: 50 / Protocol: FLEXIBLE FIT / Space: REAL |