6SC2

Structure of the dynein-2 complex; IFT-train bound model


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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 of the dynein-2 complex and its assembly with intraflagellar transport trains.

Toropova, K.Zalyte, R.Mukhopadhyay, A.G.Mladenov, M.Carter, A.P.Roberts, A.J.

(2019) Nat Struct Mol Biol 26: 823-829

  • DOI: https://doi.org/10.1038/s41594-019-0286-y
  • Primary Citation of Related Structures:  
    6RLA, 6RLB, 6SC2

  • PubMed 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 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.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK. a.roberts@mail.cryst.bbk.ac.uk.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA alkyltransferase mutant,Cytoplasmic dynein 2 heavy chain 1,DYNC2H1 variant protein,DYNC2H1 variant protein,DYNC2H1 variant protein4,513Homo sapiensMutation(s): 0 
UniProt
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsE5BBQ0B0I1S0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA alkyltransferase mutant,Cytoplasmic dynein 2 heavy chain 1,DYNC2H1 variant protein,DYNC2H1 variant protein,DYNC2H1 variant protein4,513Homo sapiensMutation(s): 0 
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UniProt GroupsE5BBQ0B0I1S0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 601,066Homo sapiensMutation(s): 0 
Gene Names: WDR60
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GTEx:  ENSG00000126870 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 34564Homo sapiensMutation(s): 0 
Gene Names: WDR34
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 2 light intermediate chain 1
E, F
351Homo sapiensMutation(s): 0 
Gene Names: DYNC2LI1D2LICLIC3CGI-60
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GTEx:  ENSG00000138036 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain roadblock-type 1
G, H
96Homo sapiensMutation(s): 0 
Gene Names: DYNLRB1BITHDNCL2ADNLC2AROBLD1HSPC162
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain 1, cytoplasmic
I, J, K, L, M
I, J, K, L, M, N
89Homo sapiensMutation(s): 0 
Gene Names: DYNLL1DLC1DNCL1DNCLC1HDLC1
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
P [auth A],
U [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
O [auth A]
R [auth A]
S [auth A]
T [auth B]
W [auth B]
O [auth A],
R [auth A],
S [auth A],
T [auth B],
W [auth B],
X [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
Q [auth A],
V [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104196/Z/14/Z
Royal SocietyUnited Kingdom104196/Z/14/Z
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P008348/1
Royal SocietyUnited KingdomRG170260
Wellcome TrustUnited KingdomWT100387
Medical Research Council (United Kingdom)United KingdomMC_UP_A025_1011
Wellcome TrustUnited Kingdom079605/Z/06/Z
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L014211/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references