9M5E | pdb_00009m5e

Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (singlet complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Activation of Arp2/3 complex by a SPIN90 dimer in linear actin-filament nucleation.

Francis, J.Pathri, A.K.Shyam, K.T.Sripada, S.Mitra, R.Narvaez-Ortiz, H.Y.Eliyan, K.V.Nolen, B.J.Chowdhury, S.

(2025) Nat Struct Mol Biol 32: 2272-2284

  • DOI: https://doi.org/10.1038/s41594-025-01673-8
  • Primary Citation of Related Structures:  
    9M5E, 9M64

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 3418Bos taurusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2394Bos taurusMutation(s): 0 
UniProt
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UniProt GroupA7MB62
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1B372Bos taurusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2300Bos taurusMutation(s): 0 
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UniProt GroupQ3MHR7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3178Bos taurusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4168Bos taurusMutation(s): 0 
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UniProt GroupQ148J6
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5151Bos taurusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NCK-interacting protein with SH3 domainH,
L [auth h]
454Homo sapiensMutation(s): 0 
Gene Names: NCKIPSDAF3P21SPIN90
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ3 (Homo sapiens)
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PHAROS:  Q9NZQ3
GTEx:  ENSG00000213672 
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UniProt GroupQ9NZQ3
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle
I, J, K
377Gallus gallusMutation(s): 0 
EC: 3.6.4
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
N [auth A],
P [auth B],
R [auth I],
T [auth J],
U [auth K]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

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M [auth A],
O [auth B],
Q [auth I],
S [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
I, J, K
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.6.2
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Council of Scientific & Industrial Research (CSIR)IndiaFBR070301
Council of Scientific & Industrial Research (CSIR)IndiaOLP0028

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Data collection, Database references
  • Version 1.2: 2025-11-26
    Changes: Data collection, Database references