6W18

Structure of S. pombe Arp2/3 complex in inactive state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state.

Shaaban, M.Chowdhury, S.Nolen, B.J.

(2020) Nat Struct Mol Biol 27: 1009-1016

  • DOI: https://doi.org/10.1038/s41594-020-0481-x
  • Primary Citation of Related Structures:  
    6W17, 6W18

  • PubMed Abstract: 

    Arp2/3 complex, a crucial actin filament nucleator, undergoes structural rearrangements during activation by nucleation-promoting factors (NPFs). However, the conformational pathway leading to the nucleation-competent state is unclear due to lack of high-resolution structures of the activated state. Here we report a ~3.9 Å resolution cryo-EM structure of activated Schizosaccharomyces pombe Arp2/3 complex bound to the S. pombe NPF Dip1 and attached to the end of the nucleated actin filament. The structure reveals global and local conformational changes that allow the two actin-related proteins in Arp2/3 complex to mimic a filamentous actin dimer and template nucleation. Activation occurs through a clamp-twisting mechanism, in which Dip1 forces two core subunits in Arp2/3 complex to pivot around one another, shifting half of the complex into a new activated position. By showing how Dip1 stimulates activation, the structure reveals how NPFs can activate Arp2/3 complex in diverse cellular processes.


  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 3427Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for P32390 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Go to UniProtKB:  P32390
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UniProt GroupP32390
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2390Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for Q9UUJ1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupQ9UUJ1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1377Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for P78774 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2317Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for O14241 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupO14241
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3174Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for Q9Y7J4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4168Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for Q92352 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5152Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for Q10316 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.12.4
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM127440, R01GM092917, S10OD012272

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references
  • Version 1.2: 2020-11-18
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Refinement description