8RGG

Structure of dynein-2 intermediate chain DYNC2I2 (WDR34) in complex with dynein-2 heavy chain DYNC2H1.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and tethering mechanism of dynein-2 intermediate chains in intraflagellar transport.

Mukhopadhyay, A.G.Toropova, K.Daly, L.Wells, J.N.Vuolo, L.Mladenov, M.Seda, M.Jenkins, D.Stephens, D.J.Roberts, A.J.

(2024) EMBO J 43: 1257-1272

  • DOI: https://doi.org/10.1038/s44318-024-00060-1
  • Primary Citation of Related Structures:  
    8RGG, 8RGH, 8RGI

  • PubMed 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. 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.


  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1A [auth B]4,513Homo sapiensMutation(s): 23 
Gene Names: MGMTDYNC2H1DHC1BDHC2DNCH2DYH1BKIAA1997
EC: 2.1.1.63
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Find proteins for P16455 (Homo sapiens)
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Go to UniProtKB:  P16455
PHAROS:  P16455
GTEx:  ENSG00000170430 
Find proteins for Q8NCM8 (Homo sapiens)
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Go to UniProtKB:  Q8NCM8
PHAROS:  Q8NCM8
GTEx:  ENSG00000187240 
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UniProt GroupsP16455Q8NCM8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 2 intermediate chain 1B [auth C]1,066Homo sapiensMutation(s): 0 
Gene Names: DYNC2I1WDR60
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GTEx:  ENSG00000126870 
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UniProt GroupQ8WVS4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 2 intermediate chain 2C [auth D]564Homo sapiensMutation(s): 0 
Gene Names: DYNC2I2WDR34
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GTEx:  ENSG00000119333 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain roadblock-type 1D [auth G],
E [auth H]
96Homo sapiensMutation(s): 0 
Gene Names: DYNLRB1BITHDNCL2ADNLC2AROBLD1HSPC162
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GTEx:  ENSG00000125971 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain 1, cytoplasmicF [auth I],
G [auth J]
89Homo sapiensMutation(s): 0 
Gene Names: DYNLL1DLC1DNCL1DNCLC1HDLC1
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GTEx:  ENSG00000088986 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom217186/Z/19/Z
Wellcome TrustUnited Kingdom206166/Z/17/Z
Wellcome TrustUnited Kingdom202679/Z/16/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P008348/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S007202/1
Royal SocietyUnited KingdomRG170260
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S013024/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S005390/1
Wellcome TrustUnited Kingdom210585/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references