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- PDB-8rgh: Structure of dynein-2 intermediate chain DYNC2I1 (WDR60) in compl... -
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Basic information
Entry | Database: PDB / ID: 8rgh | ||||||||||||||||||||||||||||||
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Title | Structure of dynein-2 intermediate chain DYNC2I1 (WDR60) in complex with the dynein-2 heavy chain DYNC2H1. | ||||||||||||||||||||||||||||||
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![]() | TRANSPORT PROTEIN / dynein / cilia / intraflagellar transport / complex | ||||||||||||||||||||||||||||||
Function / homology | ![]() MGMT-mediated DNA damage reversal / intraciliary transport involved in cilium assembly / visual behavior / intraciliary retrograde transport / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / cilium movement involved in cell motility / 9+2 motile cilium / intraciliary transport / dynein light chain binding ...MGMT-mediated DNA damage reversal / intraciliary transport involved in cilium assembly / visual behavior / intraciliary retrograde transport / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / cilium movement involved in cell motility / 9+2 motile cilium / intraciliary transport / dynein light chain binding / ciliary transition zone / regulation of cilium assembly / spinal cord motor neuron differentiation / dynein heavy chain binding / DNA-methyltransferase activity / embryonic skeletal system morphogenesis / ciliary tip / Intraflagellar transport / dynein complex / DNA ligation / coronary vasculature development / minus-end-directed microtubule motor activity / non-motile cilium assembly / DNA alkylation repair / dynein light intermediate chain binding / protein localization to cilium / cytoplasmic dynein complex / positive regulation of smoothened signaling pathway / ciliary plasm / dorsal/ventral pattern formation / motile cilium / determination of left/right symmetry / embryonic limb morphogenesis / positive regulation of double-strand break repair / microtubule motor activity / ciliary base / dynein intermediate chain binding / pericentriolar material / microtubule-based movement / Golgi organization / cytoskeletal motor activity / axoneme / cilium assembly / Hedgehog 'off' state / forebrain development / centriole / ciliary basal body / filopodium / kidney development / methyltransferase activity / cilium / protein processing / apical part of cell / methylation / microtubule / DNA repair / centrosome / negative regulation of apoptotic process / Golgi apparatus / ATP hydrolysis activity / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||||||||||||||||||||
![]() | Mukhopadhyay, A.G. / Toropova, K. / Daly, L. / Wells, J. / Vuolo, L. / Seda, M. / Jenkins, D. / Stephens, D.J. / Roberts, A.J. | ||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and tethering mechanism of dynein-2 intermediate chains in intraflagellar transport. Authors: Aakash G Mukhopadhyay / Katerina Toropova / Lydia Daly / Jennifer N Wells / Laura Vuolo / Miroslav Mladenov / Marian Seda / Dagan Jenkins / David J Stephens / Anthony J Roberts / ![]() Abstract: Dynein-2 is a large multiprotein complex that powers retrograde intraflagellar transport (IFT) of cargoes within cilia/flagella, but the molecular mechanism underlying this function is still emerging. ...Dynein-2 is a large multiprotein complex that powers retrograde intraflagellar transport (IFT) of cargoes within cilia/flagella, but the molecular mechanism underlying this function is still emerging. Distinctively, dynein-2 contains two identical force-generating heavy chains that interact with two different intermediate chains (WDR34 and WDR60). Here, we dissect regulation of dynein-2 function by WDR34 and WDR60 using an integrative approach including cryo-electron microscopy and CRISPR/Cas9-enabled cell biology. A 3.9 Å resolution structure shows how WDR34 and WDR60 use surprisingly different interactions to engage equivalent sites of the two heavy chains. We show that cilia can assemble in the absence of either WDR34 or WDR60 individually, but not both subunits. Dynein-2-dependent distribution of cargoes depends more strongly on WDR60, because the unique N-terminal extension of WDR60 facilitates dynein-2 targeting to cilia. Strikingly, this N-terminal extension can be transplanted onto WDR34 and retain function, suggesting it acts as a flexible tether to the IFT "trains" that assemble at the ciliary base. We discuss how use of unstructured tethers represents an emerging theme in IFT train interactions. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 347.1 KB | Display | ![]() |
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PDB format | ![]() | 206.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 51.4 KB | Display | |
Data in CIF | ![]() | 78.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 19133MC ![]() 8rggC ![]() 8rgiC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 515223.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DYNC2H1 with N-terminal SNAPf tag / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P16455, UniProt: Q8NCM8, methylated-DNA-[protein]-cysteine S-methyltransferase |
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#2: Protein | Mass: 122865.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 60639.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DYNC2I2 (also known as WDR34) with C-terminal Strep tag Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 39681.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 10934.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Dynein-2 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113479 / Details: Global resolution 3.9A / Symmetry type: POINT |