8RGI

Structure of DYNLT1:DYNLT2B (TCTEX1:TCTEX1D2) heterodimer.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.259 

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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain Tctex-type 1113Homo sapiensMutation(s): 0 
Gene Names: DYNLT1TCTEL1TCTEX-1TCTEX1
UniProt & NIH Common Fund Data Resources
Find proteins for P63172 (Homo sapiens)
Explore P63172 
Go to UniProtKB:  P63172
PHAROS:  P63172
GTEx:  ENSG00000146425 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63172
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain Tctex-type protein 2B142Homo sapiensMutation(s): 0 
Gene Names: DYNLT2BTCTEX1D2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WW35 (Homo sapiens)
Explore Q8WW35 
Go to UniProtKB:  Q8WW35
PHAROS:  Q8WW35
GTEx:  ENSG00000213123 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WW35
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.259 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.149α = 90
b = 78.149β = 90
c = 112.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom217186/Z/19/Z
Wellcome TrustUnited Kingdom221543/Z/20/Z
Royal SocietyUnited KingdomRG170260
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P008348/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S007202/1
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