5NW4

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
dynein heavy chain
B
889N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
dynein intermediate chain
D
341N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
dynein intermediate chain
C
350N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
dynein heavy chain
A
922N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
dynein N-terminal dimerization domain
1
125N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
dynein N-terminal dimerization domain
2
124N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Robl
R, S
120N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
dynein light intermediate chain
E
295N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
dynein light intermediate chain
F
298N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Arp1
G, H, O, P, Q, T, U, W
376Sus scrofaGene Names: ACTR1A
Find proteins for F2Z5G5 (Sus scrofa)
Go to Gene View: ACTR1A
Go to UniProtKB:  F2Z5G5
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
beta-actin
V
396Alligator mississippiensis
Find proteins for A0A151MAL5 (Alligator mississippiensis)
Go to UniProtKB:  A0A151MAL5
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Arp11
X
417Sus scrofaGene Names: ACTR10
Find proteins for I3LHK5 (Sus scrofa)
Go to Gene View: ACTR10
Go to UniProtKB:  I3LHK5
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Capping protein (Actin filament) muscle Z-line, alpha 1
Y
286Sus scrofaGene Names: CP alpha1 (Capza, CAPZA1)
Find proteins for A0PFK5 (Sus scrofa)
Go to UniProtKB:  A0PFK5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
F-actin capping protein beta subunit variant II
Z
293Sus scrofaGene Names: CAPZB
Find proteins for D2JYW4 (Sus scrofa)
Go to Gene View: CAPZB
Go to UniProtKB:  D2JYW4
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
dynactin shoulder complex
a
571N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
dynactin shoulder complex
b
602N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
dynactin shoulder complex
c, d
130N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
dynactin shoulder complex
e, f
174N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Dynactin 6
g
190Sus scrofaGene Names: DCTN6
Find proteins for D0G6S1 (Sus scrofa)
Go to Gene View: DCTN6
Go to UniProtKB:  D0G6S1
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Dynactin subunit 5
h
222Homo sapiensGene Names: DCTN5
Find proteins for Q9BTE1 (Homo sapiens)
Go to Gene View: DCTN5
Go to UniProtKB:  Q9BTE1
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
dynactin pointed end p62
i
243N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
p150
j
52N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Dynactin
k
48Sus scrofa
Find proteins for A0A0J9X292 (Sus scrofa)
Go to UniProtKB:  A0A0J9X292
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Dynactin
l
71Sus scrofa
Find proteins for A0A0J9X293 (Sus scrofa)
Go to UniProtKB:  A0A0J9X293
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Dynactin
m
31Sus scrofa
Find proteins for A0A0J9X299 (Sus scrofa)
Go to UniProtKB:  A0A0J9X299
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Dynactin
n
20Sus scrofa
Find proteins for A0A0J9X293 (Sus scrofa)
Go to UniProtKB:  A0A0J9X293
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
dynactin p150
o
53N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
BICD2N
5, 6
275N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
1, 2, 5, 6, a, A, B, b, c, C, d, D, E, e, f, F, i, j, o, R, S
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence