5NVU

Full length human cytoplasmic dynein-1 in the phi-particle conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated.

Zhang, K.Foster, H.E.Rondelet, A.Lacey, S.E.Bahi-Buisson, N.Bird, A.W.Carter, A.P.

(2017) Cell 169: 1303-1314.e18

  • DOI: https://doi.org/10.1016/j.cell.2017.05.025
  • Primary Citation of Related Structures:  
    5NUG, 5NVS, 5NVU, 5NW4

  • PubMed Abstract: 

    Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves poorly on its own or how it is activated by dynactin. Here, we present a cryoelectron microscopy structure of the complete 1.4-megadalton human dynein-1 complex in an inhibited state known as the phi-particle. We reveal the 3D structure of the cargo binding dynein tail and show how self-dimerization of the motor domains locks them in a conformation with low microtubule affinity. Disrupting motor dimerization with structure-based mutagenesis drives dynein-1 into an open form with higher affinity for both microtubules and dynactin. We find the open form is also inhibited for movement and that dynactin relieves this by reorienting the motor domains to interact correctly with microtubules. Our model explains how dynactin binding to the dynein-1 tail directly stimulates its motor activity.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein motor domain
A, B
3,169Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein tail heavy chain932Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein intermediate chain
D, E
350Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein tail heavy chain893Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light intermediate chain298Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light intermediate chain295Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal dimerization domain125Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal dimerization domain124Homo sapiensMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
LC8
K, L
85Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Tctex103Homo sapiensMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Tctex104Homo sapiensMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Intermediate chain N-terminus peptides27Homo sapiensMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Intermediate chain N-terminus peptides29Homo sapiensMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Robl
Q, R
120Homo sapiensMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT100387
Medical Research Council (United Kingdom)United KingdomMC_UP_A025_1011

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2017-09-06
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary