6ZNL

Cryo-EM structure of the dynactin complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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 the complex architecture of dynactin's shoulder region and pointed end.

Lau, C.K.O'Reilly, F.J.Santhanam, B.Lacey, S.E.Rappsilber, J.Carter, A.P.

(2021) EMBO J 40: e106164-e106164

  • DOI: https://doi.org/10.15252/embj.2020106164
  • Primary Citation of Related Structures:  
    6ZNL, 6ZNM, 6ZNN, 6ZNO, 6ZO4

  • PubMed Abstract: 

    Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled-coil adaptor. Dynactin consists of an actin-related filament whose length is defined by its flexible shoulder domain. Despite previous cryo-EM structures, the molecular architecture of the shoulder and pointed end of the filament is still poorly understood due to the lack of high-resolution information in these regions. Here we combine multiple cryo-EM datasets and define precise masking strategies for particle signal subtraction and 3D classification. This overcomes domain flexibility and results in high-resolution maps into which we can build the shoulder and pointed end. The unique architecture of the shoulder securely houses the p150 subunit and positions the four identical p50 subunits in different conformations to bind dynactin's filament. The pointed end map allows us to build the first structure of p62 and reveals the molecular basis for cargo adaptor binding to different sites at the pointed end.


  • Organizational Affiliation

    Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ARP1 actin related protein 1 homolog A
A, B, C, D, E
A, B, C, D, E, F, G, I
376Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupF2Z5G5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1375Sus scrofaMutation(s): 0 
UniProt
Find proteins for Q6QAQ1 (Sus scrofa)
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UniProt GroupQ6QAQ1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Arp11417Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capping protein (Actin filament) muscle Z-line, alpha 1286Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0PFK5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
F-actin capping protein beta subunit272Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 2M,
N,
T [auth m],
U [auth n]
405Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0A5G2QD80
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 3O,
V [auth o]
186Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin 6P [auth U]190Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupD0G6S1
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 5Q [auth V]182Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 4R [auth Y]467Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 1S [auth Z],
W [auth z]
1,286Sus scrofaMutation(s): 0 
UniProt
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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EA [auth H]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

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AA [auth D]
BA [auth E]
CA [auth F]
DA [auth G]
FA [auth I]
AA [auth D],
BA [auth E],
CA [auth F],
DA [auth G],
FA [auth I],
GA [auth J],
X [auth A],
Y [auth B],
Z [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

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HA [auth Y],
IA [auth Y],
JA [auth Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2021-04-28
    Changes: Database references