5NW4

Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 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 heavy chainA [auth B]889Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
dynein intermediate chainB [auth D]341Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
dynein intermediate chain350Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
dynein heavy chainD [auth A]922Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
dynein N-terminal dimerization domainE [auth 1]125Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
dynein N-terminal dimerization domainF [auth 2]124Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RoblG [auth R],
H [auth S]
120Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
dynein light intermediate chainI [auth E]295Homo sapiensMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
dynein light intermediate chainJ [auth F]298Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Arp1376Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupF2Z5G5
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
beta-actinR [auth V]396Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A151MAL5 (Alligator mississippiensis)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Arp11T [auth X]417Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Capping protein (Actin filament) muscle Z-line, alpha 1U [auth Y]286Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
F-actin capping protein beta subunit variant IIV [auth Z]293Sus scrofaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
dynactin shoulder complexW [auth a]571Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
dynactin shoulder complexX [auth b]602Sus scrofaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
dynactin shoulder complexY [auth c],
Z [auth d]
130Sus scrofaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
dynactin shoulder complexAA [auth e],
BA [auth f]
174Sus scrofaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin 6CA [auth g]190Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 5DA [auth h]222Sus scrofaMutation(s): 0 
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GTEx:  ENSG00000166847 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
dynactin pointed end p62EA [auth i]243Sus scrofaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
p150FA [auth j]52Sus scrofaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
DynactinGA [auth k]48Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
DynactinHA [auth l]71Sus scrofaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
DynactinIA [auth m]31Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
DynactinJA [auth n]20Sus scrofaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
dynactin p150KA [auth o]53Sus scrofaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
BICD2NLA [auth 5],
MA [auth 6]
275Homo sapiensMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 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 KingdomWT100387
Medical Research Council (United Kingdom)United KingdomMC_UP_A025_1011

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations