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- PDB-9i2b: SPIN90-Arp2/3 nucleated bidirectional actin filaments -

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Basic information

Entry
Database: PDB / ID: 9i2b
TitleSPIN90-Arp2/3 nucleated bidirectional actin filaments
Components
  • (Actin-related protein ...) x 7
  • Actin, cytoplasmic 1
  • NCK-interacting protein with SH3 domain
  • Phalloidin
KeywordsCYTOSOLIC PROTEIN / Cytoskeleton / Branched actin network
Function / homology
Function and homology information


tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / spindle localization / meiotic cytokinesis / actin polymerization-dependent cell motility / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions ...tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / spindle localization / meiotic cytokinesis / actin polymerization-dependent cell motility / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / UCH proteinases / muscle cell projection membrane / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / asymmetric cell division / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / actin nucleation / Arp2/3 complex binding / actin cap / cellular response to cytochalasin B / regulation of actin filament polymerization / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / postsynaptic actin cytoskeleton / Tat protein binding / adherens junction assembly / apical protein localization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / intermediate filament / tight junction / apical junction complex / regulation of norepinephrine uptake / transporter regulator activity / nitric-oxide synthase binding / cortical cytoskeleton / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / positive regulation of actin filament polymerization / filamentous actin / brush border / kinesin binding / regulation of postsynapse assembly / cilium assembly / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / cytoskeletal protein binding / actin filament polymerization / EPHB-mediated forward signaling / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / cell projection / adherens junction / FCGR3A-mediated phagocytosis / actin filament / cell motility / positive regulation of neuron projection development / cellular response to nerve growth factor stimulus / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / SH3 domain binding / cellular response to type II interferon / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to estrogen / Schaffer collateral - CA1 synapse / cytoplasmic ribonucleoprotein granule / endocytosis / actin filament binding / azurophil granule lumen / cell-cell junction / synaptic vesicle membrane / Clathrin-mediated endocytosis / cell migration / nucleosome / site of double-strand break / response to estradiol / lamellipodium / actin cytoskeleton / actin binding / cell cortex / ficolin-1-rich granule lumen / cytoskeleton / neuron projection
Similarity search - Function
SPIN90, SH3 domain / SPIN90/Ldb17, leucine-rich domain / SPIN90/Ldb17 / SPIN90/Ldb17, leucine-rich domain / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 ...SPIN90, SH3 domain / SPIN90/Ldb17, leucine-rich domain / SPIN90/Ldb17 / SPIN90/Ldb17, leucine-rich domain / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 20 kDa subunit (ARPC4) / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / ATPase, nucleotide binding domain / Src homology 3 (SH3) domain profile. / SH3 domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin-related protein 2/3 complex subunit 1B / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 3 / Actin-related protein 2 / Actin, cytoplasmic 1 / Actin-related protein 2/3 complex subunit 5-like protein / NCK-interacting protein with SH3 domain
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
Amanita phalloides (death cap)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLiu, T. / Moores, C.A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers.
Authors: Tianyang Liu / Luyan Cao / Miroslav Mladenov / Guillaume Romet-Lemonne / Michael Way / Carolyn A Moores /
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- ...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.
History
DepositionJan 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Actin-related protein 2
D: Actin-related protein 2/3 complex subunit 2
E: Actin-related protein 2/3 complex subunit 3
F: Actin-related protein 2/3 complex subunit 4
G: Actin-related protein 2/3 complex subunit 5-like protein
I: Actin, cytoplasmic 1
J: Actin, cytoplasmic 1
c: Phalloidin
d: Phalloidin
H: NCK-interacting protein with SH3 domain
C: Actin-related protein 2/3 complex subunit 1B
A: Actin-related protein 3
L: Actin-related protein 2
N: Actin-related protein 2/3 complex subunit 2
O: Actin-related protein 2/3 complex subunit 3
P: Actin-related protein 2/3 complex subunit 4
Q: Actin-related protein 2/3 complex subunit 5-like protein
S: Actin, cytoplasmic 1
T: Actin, cytoplasmic 1
U: Phalloidin
V: Phalloidin
R: NCK-interacting protein with SH3 domain
M: Actin-related protein 2/3 complex subunit 1B
K: Actin-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)781,82940
Polymers778,21724
Non-polymers3,61216
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Actin-related protein ... , 7 types, 14 molecules BLDNEOFPGQCMAK

#1: Protein Actin-related protein 2 / Actin-like protein 2


Mass: 44818.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR2, ARP2 / Production host: unidentified baculovirus / References: UniProt: P61160
#2: Protein Actin-related protein 2/3 complex subunit 2 / Arp2/3 complex 34 kDa subunit / p34-ARC


Mass: 34386.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC2, ARC34, PRO2446 / Production host: unidentified baculovirus / References: UniProt: O15144
#3: Protein Actin-related protein 2/3 complex subunit 3 / Arp2/3 complex 21 kDa subunit / p21-ARC


Mass: 20572.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC3, ARC21 / Production host: unidentified baculovirus / References: UniProt: O15145
#4: Protein Actin-related protein 2/3 complex subunit 4 / Arp2/3 complex 20 kDa subunit / p20-ARC


Mass: 19697.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC4, ARC20 / Production host: unidentified baculovirus / References: UniProt: P59998
#5: Protein Actin-related protein 2/3 complex subunit 5-like protein / Arp2/3 complex 16 kDa subunit 2 / ARC16-2


Mass: 16964.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC5L / Production host: unidentified baculovirus / References: UniProt: Q9BPX5
#9: Protein Actin-related protein 2/3 complex subunit 1B / Arp2/3 complex 41 kDa subunit / p41-ARC


Mass: 41004.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC1B, ARC41 / Production host: unidentified baculovirus / References: UniProt: O15143
#10: Protein Actin-related protein 3 / Actin-like protein 3


Mass: 47428.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR3, ARP3 / Production host: unidentified baculovirus / References: UniProt: P61158

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Protein , 2 types, 6 molecules IJSTHR

#6: Protein
Actin, cytoplasmic 1 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1
#8: Protein NCK-interacting protein with SH3 domain / 54 kDa VacA-interacting protein / 54 kDa vimentin-interacting protein / VIP54 / 90 kDa SH3 protein ...54 kDa VacA-interacting protein / 54 kDa vimentin-interacting protein / VIP54 / 90 kDa SH3 protein interacting with Nck / AF3p21 / Dia-interacting protein 1 / DIP-1 / Diaphanous protein-interacting protein / SH3 adapter protein SPIN90 / WASP-interacting SH3-domain protein / WISH / Wiskott-Aldrich syndrome protein-interacting protein


Mass: 79054.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCKIPSD, AF3P21, SPIN90 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ3

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Protein/peptide , 1 types, 4 molecules cdUV

#7: Protein/peptide
Phalloidin


Mass: 808.899 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Amanita phalloides (death cap)

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Non-polymers , 2 types, 16 molecules

#11: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#12: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1The SPIN90-Arp2/3 complex in the presence of actinCOMPLEX#1-#100RECOMBINANT
2The Arp2/3 complexCOMPLEX#1-#5, #9-#101RECOMBINANT
3Actin, cytoplasmic 1COMPLEX#61NATURAL
4PhalloidinCOMPLEX#71NATURAL
5SPIN90COMPLEX#81RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Sus scrofa (pig)9823
54Amanita phalloides (death cap)67723
65Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21unidentified baculovirus10469
32unidentified baculovirus10469
43unidentified baculovirus10469
54unidentified baculovirus10469
65Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 39.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2Topazparticle selection
3EPUimage acquisition
5cryoSPARCCTF correction
8Cootmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39104 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER

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