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- EMDB-63886: Focused actin filament map of SPIN90 dimer-Arp2/3 complex-filamen... -

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Basic information

Entry
Database: EMDB / ID: EMD-63886
TitleFocused actin filament map of SPIN90 dimer-Arp2/3 complex-filament singlet complex structure
Map dataMasked sharpened filament focused map
Sample
  • Complex: Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (Singlet Complex)
KeywordsSPIN90 / actin / cytoskeleton / Arp2-3 complex / Nucleation Promoting Factor / CYTOSOLIC PROTEIN
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFrancis J / Pathri AK / Chowdhury S
Funding support India, 2 items
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 22, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63886.png

Downloads & links

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Map

FileDownload / File: emd_63886.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMasked sharpened filament focused map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.193
Minimum - Maximum-0.6766894 - 1.3754472
Average (Standard dev.)0.0011293306 (±0.024600813)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63886_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unmasked sharpened filament focused map

Fileemd_63886_additional_1.map
AnnotationUnmasked sharpened filament focused map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened, unmasked filament focused map

Fileemd_63886_additional_2.map
AnnotationUnsharpened, unmasked filament focused map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Masked Odd half map

Fileemd_63886_half_map_1.map
AnnotationMasked Odd half map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Masked Even half map

Fileemd_63886_half_map_2.map
AnnotationMasked Even half map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament...

EntireName: Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (Singlet Complex)
Components
  • Complex: Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (Singlet Complex)

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Supramolecule #1: Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament...

SupramoleculeName: Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (Singlet Complex)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 100 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 3 / Number real images: 24000 / Average exposure time: 7.19 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Software - details: Patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction from Cryosparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 28368
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7tpt


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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