9M5E image
Deposition Date 2025-03-05
Release Date 2025-09-10
Last Version Date 2025-11-26
Entry Detail
PDB ID:
9M5E
Title:
Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (singlet complex)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Bos taurus (Taxon ID: 9913)
Gallus gallus (Taxon ID: 9031)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.55 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 3
Gene (Uniprot):ACTR3
Chain IDs:A
Chain Length:418
Number of Molecules:1
Biological Source:Bos taurus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2
Gene (Uniprot):ACTR2
Chain IDs:B
Chain Length:394
Number of Molecules:1
Biological Source:Bos taurus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2/3 complex subunit 1B
Gene (Uniprot):ARPC1B
Chain IDs:C
Chain Length:372
Number of Molecules:1
Biological Source:Bos taurus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2/3 complex subunit 2
Gene (Uniprot):ARPC2
Chain IDs:D
Chain Length:300
Number of Molecules:1
Biological Source:Bos taurus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2/3 complex subunit 3
Gene (Uniprot):ARPC3
Chain IDs:E
Chain Length:178
Number of Molecules:1
Biological Source:Bos taurus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2/3 complex subunit 4
Gene (Uniprot):ARPC4
Chain IDs:F
Chain Length:168
Number of Molecules:1
Biological Source:Bos taurus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Actin-related protein 2/3 complex subunit 5
Gene (Uniprot):ARPC5
Chain IDs:G
Chain Length:151
Number of Molecules:1
Biological Source:Bos taurus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NCK-interacting protein with SH3 domain
Gene (Uniprot):NCKIPSD
Chain IDs:H, L (auth: h)
Chain Length:454
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Actin, alpha skeletal muscle
Gene (Uniprot):ACTA1
Chain IDs:I, J, K
Chain Length:377
Number of Molecules:3
Biological Source:Gallus gallus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
HIC I HIS modified residue
Primary Citation
Activation of Arp2/3 complex by a SPIN90 dimer in linear actin-filament nucleation.
Nat.Struct.Mol.Biol. 32 2272 2284 (2025)
PMID: 40954370 DOI: 10.1038/s41594-025-01673-8

Abstact

Arp2/3 complex is a key nucleator of actin filaments. It requires activation by nucleation-promoting factors (NPFs). WISH/DIP1/SPIN90 (WDS) proteins represent a unique class of NPFs that activate the Arp2/3 complex independently of preexisting filaments, promoting linear actin-filament nucleation. In fission yeast, Dip1 binds to the clamp subunits in Arp2/3 complex to induce the short-pitch conformation, where Arp2 moves closer to Arp3 to mimic a filamentous actin dimer. However, how WDS proteins stimulate subunit flattening in Arp subunits, a 'scissor-like' conformational change akin to what is observed in an actin monomer during filament formation, remained unclear. Here we present cryo-electron microscopy structures of human SPIN90 bound to activated bovine Arp2/3 complex on an actin filament pointed end. The structures show that SPIN90 dimerizes through a metazoan-specific domain in the middle segment, engaging both the clamp and the Arp3/ARPC3 interface, to drive the activating conformational changes in Arp2/3 complex. Remarkably, a single SPIN90 dimer can also bridge two Arp2/3 complexes, enabling bidirectional actin nucleation and suggesting a mechanism for rapidly assembling complex actin network architectures.

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