+Open data
-Basic information
Entry | Database: PDB / ID: 6rla | |||||||||||||||||||||||||||
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Title | Structure of the dynein-2 complex; motor domains | |||||||||||||||||||||||||||
Components | O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein | |||||||||||||||||||||||||||
Keywords | MOTOR PROTEIN / dynein / cilia / intraflagellar transport / complex | |||||||||||||||||||||||||||
Function / homology | Function and homology information methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / dynein complex / cell projection organization / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / dynein intermediate chain binding / microtubule-based movement / cilium / methylation ...methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / dynein complex / cell projection organization / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / dynein intermediate chain binding / microtubule-based movement / cilium / methylation / microtubule / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||||||||||||||||||||
Authors | Toropova, K. / Zalyte, R. / Mukhopadhyay, A.G. / Mladenov, M. / Carter, A.P. / Roberts, A.J. | |||||||||||||||||||||||||||
Funding support | United Kingdom, 8items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Structure of the dynein-2 complex and its assembly with intraflagellar transport trains. Authors: Katerina Toropova / Ruta Zalyte / Aakash G Mukhopadhyay / Miroslav Mladenov / Andrew P Carter / Anthony J Roberts / Abstract: Dynein-2 assembles with polymeric intraflagellar transport (IFT) trains to form a transport machinery that is crucial for cilia biogenesis and signaling. Here we recombinantly expressed the ~1.4-MDa ...Dynein-2 assembles with polymeric intraflagellar transport (IFT) trains to form a transport machinery that is crucial for cilia biogenesis and signaling. Here we recombinantly expressed the ~1.4-MDa human dynein-2 complex and solved its cryo-EM structure to near-atomic resolution. The two identical copies of the dynein-2 heavy chain are contorted into different conformations by a WDR60-WDR34 heterodimer and a block of two RB and six LC8 light chains. One heavy chain is steered into a zig-zag conformation, which matches the periodicity of the anterograde IFT-B train. Contacts between adjacent dyneins along the train indicate a cooperative mode of assembly. Removal of the WDR60-WDR34-light chain subcomplex renders dynein-2 monomeric and relieves autoinhibition of its motility. Our results converge on a model in which an unusual stoichiometry of non-motor subunits controls dynein-2 assembly, asymmetry, and activity, giving mechanistic insight into the interaction of dynein-2 with IFT trains and the origin of diverse functions in the dynein family. | |||||||||||||||||||||||||||
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 | 6rla.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6rla.ent.gz | 789 KB | Display | PDB format |
PDBx/mmJSON format | 6rla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rla_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6rla_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6rla_validation.xml.gz | 142.2 KB | Display | |
Data in CIF | 6rla_validation.cif.gz | 218.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/6rla ftp://data.pdbj.org/pub/pdb/validation_reports/rl/6rla | HTTPS FTP |
-Related structure data
Related structure data | 4917MC 4918C 6rlbC 6sc2C 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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-Components
#1: Protein | Mass: 515223.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: E5BBQ0, UniProt: B0I1S0 #2: Chemical | ChemComp-ADP / #3: Chemical | #4: Chemical | Has ligand of interest | N | |
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-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-2 complex; motor domains / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 magnification: 105000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 49.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) Details: Average electron dose per image (e-/A2) for additional datasets was 46.8 and 45.4 |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57265 / Symmetry type: POINT |