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- PDB-9m64: Structure of SPIN90 dimer-Arp2/3 complexes-nucleated actin filame... -

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Basic information

Entry
Database: PDB / ID: 9m64
TitleStructure of SPIN90 dimer-Arp2/3 complexes-nucleated actin filaments (Doublet Complex)
Components
  • (Actin-related protein ...) x 7
  • Actin, alpha skeletal muscle
  • NCK-interacting protein with SH3 domain
KeywordsCYTOSOLIC PROTEIN / SPIN90 / actin / cytoskeleton / Arp2-3 complex / Nucleation Promoting Factor
Function / homology
Function and homology information


muscle cell projection membrane / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / Striated Muscle Contraction / regulation of actin filament polymerization / Clathrin-mediated endocytosis ...muscle cell projection membrane / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / Striated Muscle Contraction / regulation of actin filament polymerization / Clathrin-mediated endocytosis / intermediate filament / Neutrophil degranulation / positive regulation of actin filament polymerization / striated muscle thin filament / skeletal muscle thin filament assembly / regulation of postsynapse assembly / cilium assembly / RHO GTPases Activate WASPs and WAVEs / positive regulation of double-strand break repair via homologous recombination / cytoskeletal protein binding / positive regulation of lamellipodium assembly / skeletal muscle fiber development / stress fiber / actin filament polymerization / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / cell projection / FCGR3A-mediated phagocytosis / actin filament / positive regulation of neuron projection development / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endocytosis / actin filament binding / synaptic vesicle membrane / cell migration / lamellipodium / actin cytoskeleton / site of double-strand break / actin binding / cell cortex / hydrolase activity / postsynapse / neuron projection / endosome / focal adhesion / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
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 / Src homology 3 (SH3) domain profile. / SH3 domain / ATPase, nucleotide binding 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 / Actin-related protein 3 / Actin, alpha skeletal muscle / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 1B / NCK-interacting protein with SH3 domain
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
Gallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFrancis, J. / Pathri, A.K. / Chowdhury, S.
Funding support India, 2items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)FBR070301 India
Council of Scientific & Industrial Research (CSIR)OLP0028 India
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Activation of Arp2/3 complex by a SPIN90 dimer in linear actin-filament nucleation.
Authors: Justus Francis / Achyutha Krishna Pathri / Kankipati Teja Shyam / Sridhar Sripada / Rishav Mitra / Heidy Y Narvaez-Ortiz / Kiran Vyshnav Eliyan / Brad J Nolen / Saikat Chowdhury /
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 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.
History
DepositionMar 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-related protein 3
B: Actin-related protein 2
C: Actin-related protein 2/3 complex subunit 1B
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
H: NCK-interacting protein with SH3 domain
I: Actin, alpha skeletal muscle
J: Actin, alpha skeletal muscle
K: Actin, alpha skeletal muscle
L: Actin, alpha skeletal muscle
a: Actin-related protein 3
b: Actin-related protein 2
c: Actin-related protein 2/3 complex subunit 1B
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
h: NCK-interacting protein with SH3 domain
i: Actin, alpha skeletal muscle
j: Actin, alpha skeletal muscle
k: Actin, alpha skeletal muscle
l: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)891,77346
Polymers886,40424
Non-polymers5,36922
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 AaBbCcDdEeFfGg

#1: Protein Actin-related protein 3 / Actin-2 / Actin-like protein 3


Mass: 47428.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61157
#2: Protein Actin-related protein 2 / Actin-like protein 2


Mass: 44818.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A7MB62
#3: Protein Actin-related protein 2/3 complex subunit 1B / Arp2/3 complex 41 kDa subunit / p41-ARC


Mass: 41030.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q58CQ2
#4: Protein Actin-related protein 2/3 complex subunit 2 / Arp2/3 complex 34 kDa subunit / p34-ARC


Mass: 34402.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3MHR7
#5: 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 natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3T035
#6: 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 natural source
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q148J6
#7: Protein Actin-related protein 2/3 complex subunit 5 / Arp2/3 complex 16 kDa subunit / p16-ARC


Mass: 16251.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3SYX9

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Protein , 2 types, 10 molecules HhIJKLijkl

#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: 50561.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is a truncated construct of human SPIN90 protein that range from residues 269-722. Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Source: (gene. exp.) Homo sapiens (human) / Gene: NCKIPSD, AF3P21, SPIN90 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ3
#9: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: Residue 73 is HIC (4-methylhistidine). Due to lack of side chain densities for Chains I and i all residues have been truncated to stubs (c-beta). Any gaps are due to unmodelled regions ...Details: Residue 73 is HIC (4-methylhistidine). Due to lack of side chain densities for Chains I and i all residues have been truncated to stubs (c-beta). Any gaps are due to unmodelled regions because of poor map quality or no density for those regions.
Source: (natural) Gallus gallus (chicken) / References: UniProt: P68139

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Non-polymers , 2 types, 22 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
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

ComponentName: Structure of SPIN90 dimer-Arp2/3 complexes-nucleated actin filaments (doublet complex)
Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.978 MDaNO
210.22 MDaNO
310.1 MDaNO
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7.19 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 24000
Image scansSampling size: 14 µm / Width: 4000 / Height: 4000

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.6.2particle selectionTemplate picker
2EPUimage acquisition
4cryoSPARC4.6.2CTF correctionPatch CTF estimation
7ISOLDEmodel fitting
8Cootmodel fitting
9UCSF ChimeraXmodel fitting
11PHENIXmodel refinement
12cryoSPARC4.6.2initial Euler assignment
13cryoSPARC4.6.2final Euler assignment
14cryoSPARC4.6.2classification
15cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27106 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7TPT

7tpt


Accession code: 7TPT / Source name: PDB / Type: experimental model

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