6W17 image
Deposition Date 2020-03-03
Release Date 2020-08-12
Last Version Date 2025-04-02
Entry Detail
PDB ID:
6W17
Title:
Structure of Dip1-activated Arp2/3 complex with nucleated actin filament
Biological Source:
Method Details:
Experimental Method:
Resolution:
3.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 3
Gene (Uniprot):act2
Chain IDs:A
Chain Length:427
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2
Gene (Uniprot):arp2
Chain IDs:B
Chain Length:390
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2/3 complex subunit 1
Gene (Uniprot):arc1
Chain IDs:C
Chain Length:377
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2/3 complex subunit 2
Gene (Uniprot):arc2
Chain IDs:D
Chain Length:317
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2/3 complex subunit 3
Gene (Uniprot):arc3
Chain IDs:E
Chain Length:174
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2/3 complex subunit 4
Gene (Uniprot):arc4
Chain IDs:F
Chain Length:168
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2/3 complex subunit 5
Gene (Uniprot):arc5
Chain IDs:G
Chain Length:152
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Polymer Type:polypeptide(L)
Molecule:Protein dip1
Gene (Uniprot):dip1
Chain IDs:H
Chain Length:374
Number of Molecules:1
Biological Source:Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Polymer Type:polypeptide(L)
Molecule:Actin, alpha skeletal muscle
Gene (Uniprot):ACTA1
Chain IDs:I, J, K, L
Chain Length:377
Number of Molecules:4
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Phalloidin
Chain IDs:M, N, O, P, Q
Chain Length:7
Number of Molecules:5
Biological Source:Amanita phalloides
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
HIC I HIS modified residue
Primary Citation
Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state.
Nat.Struct.Mol.Biol. 27 1009 1016 (2020)
PMID: 32839613 DOI: 10.1038/s41594-020-0481-x

Abstact

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.

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Primary Citation of related structures