9I2B | pdb_00009i2b

SPIN90-Arp2/3 nucleated bidirectional actin filaments


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers.

Liu, T.Cao, L.Mladenov, M.Romet-Lemonne, G.Way, M.Moores, C.A.

(2025) Nat Struct Mol Biol 32: 2262-2271

  • DOI: https://doi.org/10.1038/s41594-025-01665-8
  • Primary Citation of Related Structures:  
    9I2B

  • PubMed Abstract: 

    Branched actin networks nucleated by the Arp2/3 complex have critical roles in various cellular processes, from cell migration to intracellular transport. However, when activated by WISH/DIP/SPIN90-family proteins, Arp2/3 nucleates linear actin filaments. Here we found that human SPIN90 is a dimer that can nucleate bidirectional actin filaments. To understand the basis for this, we determined a 3-Å-resolution structure of human SPIN90-Arp2/3 complex nucleating actin filaments. Our structure shows that SPIN90 dimerizes through a three-helix bundle and interacts with two Arp2/3 complexes. Each SPIN90 molecule binds both Arp2/3 complexes to promote their activation. Our analysis demonstrates that single-filament nucleation by Arp2/3 is mechanistically more like branch formation than previously appreciated. The dimerization domain in SPIN90 orthologs is conserved in metazoans, suggesting that this mode of bidirectional nucleation is a common strategy to generate antiparallel actin filaments.


  • Organizational Affiliation
    • Institute of Structural and Molecular Biology, Birkbeck College, London, UK.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2A [auth B],
M [auth L]
394Homo sapiensMutation(s): 0 
Gene Names: ACTR2ARP2
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PHAROS:  P61160
GTEx:  ENSG00000138071 
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UniProt GroupP61160
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2B [auth D],
N
300Homo sapiensMutation(s): 0 
Gene Names: ARPC2ARC34PRO2446
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PHAROS:  O15144
GTEx:  ENSG00000163466 
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UniProt GroupO15144
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3C [auth E],
O
178Homo sapiensMutation(s): 0 
Gene Names: ARPC3ARC21
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PHAROS:  O15145
GTEx:  ENSG00000111229 
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UniProt GroupO15145
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4D [auth F],
P
168Homo sapiensMutation(s): 0 
Gene Names: ARPC4ARC20
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GTEx:  ENSG00000241553 
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UniProt GroupP59998
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5-like proteinE [auth G],
Q
153Homo sapiensMutation(s): 0 
Gene Names: ARPC5L
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PHAROS:  Q9BPX5
GTEx:  ENSG00000136950 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1F [auth I],
G [auth J],
R [auth S],
S [auth T]
375Sus scrofaMutation(s): 0 
EC: 3.6.4
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PhalloidinH [auth c],
I [auth d],
T [auth U],
U [auth V]
7Amanita phalloidesMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NCK-interacting protein with SH3 domainJ [auth H],
V [auth R]
722Homo sapiensMutation(s): 0 
Gene Names: NCKIPSDAF3P21SPIN90
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GTEx:  ENSG00000213672 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1BK [auth C],
W [auth M]
372Homo sapiensMutation(s): 0 
Gene Names: ARPC1BARC41
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GTEx:  ENSG00000130429 
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UniProt GroupO15143
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 3L [auth A],
X [auth K]
418Homo sapiensMutation(s): 0 
Gene Names: ACTR3ARP3
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PHAROS:  P61158
GTEx:  ENSG00000115091 
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth I]
CA [auth J]
EA [auth A]
GA [auth L]
IA [auth S]
AA [auth I],
CA [auth J],
EA [auth A],
GA [auth L],
IA [auth S],
KA [auth T],
MA [auth K],
Y [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth I]
DA [auth J]
FA [auth A]
HA [auth L]
JA [auth S]
BA [auth I],
DA [auth J],
FA [auth A],
HA [auth L],
JA [auth S],
LA [auth T],
NA [auth K],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
H [auth c],
I [auth d],
T [auth U],
U [auth V]
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Data collection, Database references
  • Version 1.2: 2025-11-26
    Changes: Data collection, Database references