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- PDB-8rgg: Structure of dynein-2 intermediate chain DYNC2I2 (WDR34) in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rgg | ||||||||||||||||||||||||||||||
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Title | Structure of dynein-2 intermediate chain DYNC2I2 (WDR34) in complex with dynein-2 heavy chain DYNC2H1. | ||||||||||||||||||||||||||||||
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![]() | TRANSPORT PROTEIN / dynein / cilia / intraflagellar transport / complex | ||||||||||||||||||||||||||||||
Function / homology | ![]() MGMT-mediated DNA damage reversal / nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / 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 ...MGMT-mediated DNA damage reversal / nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / 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 / spinal cord motor neuron differentiation / motile cilium assembly / dynein heavy chain binding / Activation of BIM and translocation to mitochondria / DNA-methyltransferase activity / embryonic skeletal system morphogenesis / ciliary tip / Intraflagellar transport / negative regulation of nitric oxide biosynthetic process / dynein complex / DNA ligation / negative regulation of phosphorylation / COPI-independent Golgi-to-ER retrograde traffic / coronary vasculature development / non-motile cilium assembly / minus-end-directed microtubule motor activity / DNA alkylation repair / protein localization to cilium / dynein light intermediate chain binding / cytoplasmic dynein complex / positive regulation of smoothened signaling pathway / ciliary plasm / dorsal/ventral pattern formation / enzyme inhibitor activity / determination of left/right symmetry / embryonic limb morphogenesis / positive regulation of double-strand break repair / microtubule motor activity / ciliary base / dynein intermediate chain binding / Macroautophagy / pericentriolar material / microtubule-based movement / cytoskeletal motor activity / Golgi organization / axoneme / positive regulation of insulin secretion involved in cellular response to glucose stimulus / tertiary granule membrane / ficolin-1-rich granule membrane / spermatid development / cilium assembly / Hedgehog 'off' state / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / forebrain development / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / substantia nigra development / MHC class II antigen presentation / centriole / AURKA Activation by TPX2 / ciliary basal body / methyltransferase activity / filopodium / kidney development / RHO GTPases Activate Formins / protein processing / mitotic spindle / kinetochore / cilium / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / apical part of cell / site of double-strand break / scaffold protein binding / methylation / microtubule / cytoskeleton / DNA repair / centrosome / apoptotic process / Neutrophil degranulation / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / ATP hydrolysis activity / mitochondrion / DNA binding Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||||||||||||||||||||||||||
![]() | Mukhopadhyay, A.G. / Toropova, K. / Daly, L. / Wells, J. / Vuolo, L. / Mladenov, M. / 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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Downloads & links
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PDBx/mmCIF format | ![]() | 307.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 47.6 KB | Display | |
Data in CIF | ![]() | 73.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 19132MC ![]() 8rghC ![]() 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: 10934.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | Mass: 10381.899 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: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113479 / Details: Global resolution 4.0A / Symmetry type: POINT |