5NUG

Motor domains from human cytoplasmic dynein-1 in the phi-particle conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 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: 10.1016/j.cell.2017.05.025
  • Primary Citation of Related Structures:  

  • 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 ...

    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

    Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.,MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.,MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. Electronic address: cartera@mrc-lmb.cam.ac.uk.,Department of Pediatric Neurology, Université Paris Descartes, Imaging Institute, INSERM U781, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytoplasmic dynein 1 heavy chain 1
A, B
4646Homo sapiensMutation(s): 0 
Gene Names: DYNC1H1 (DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325)
Find proteins for Q14204 (Homo sapiens)
Go to Gene View: DYNC1H1
Go to UniProtKB:  Q14204
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Data collection, Derived calculations
  • Version 1.2: 2018-10-17
    Type: Data collection, Refinement description
  • Version 1.3: 2019-10-23
    Type: Data collection, Other