6RZB

Cryo-EM structure of mouse cytoplasmic dynein-1 microtubule binding domain bound to microtubules


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM of dynein microtubule-binding domains shows how an axonemal dynein distorts the microtubule.

Lacey, S.E.He, S.Scheres, S.H.Carter, A.P.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.47145
  • Primary Citation of Related Structures:  
    6RZA, 6RZB

  • PubMed Abstract: 

    Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain (MTBD) at the end of a coiled-coil stalk. We address how cytoplasmic and axonemal dynein MTBDs bind microtubules at near atomic resolution. We decorated microtubules with MTBDs of cytoplasmic dynein-1 and axonemal dynein DNAH7 and determined their cryo-EM structures using helical Relion. The majority of the MTBD is rigid upon binding, with the transition to the high-affinity state controlled by the movement of a single helix at the MTBD interface. DNAH7 contains an 18-residue insertion, found in many axonemal dyneins, that contacts the adjacent protofilament. Unexpectedly, we observe that DNAH7, but not dynein-1, induces large distortions in the microtubule cross-sectional curvature. This raises the possibility that dynein coordination in axonemes is mediated via conformational changes in the microtubule.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain437Sus scrofaMutation(s): 0 
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
Go to UniProtKB:  Q2XVP4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain426Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Go to UniProtKB:  P02554
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MKIAA0325 protein149Mus musculusMutation(s): 2 
Gene Names: Dync1h1Dnchc1mKIAA0325
UniProt & NIH Common Fund Data Resources
Find proteins for Q9JHU4 (Mus musculus)
Go to UniProtKB:  Q9JHU4
IMPC:  MGI:103147
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTREFMAC5

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_UP_A025_1011
Wellcome TrustUnited KingdomWT210711

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection, Database references, Refinement description