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- EMDB-53106: Cryo-EM structure of the fully cofilin-1-decorated actin filament... -

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Entry
Database: EMDB / ID: EMD-53106
TitleCryo-EM structure of the fully cofilin-1-decorated actin filament (cofilactin)
Map dataMain, sharpened cryo-EM density map of the fully cofilin-1-decorated actin filament
Sample
  • Complex: Beta-actin filament fully decorated by Cofilin-1.
    • Complex: Actin filament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsactin / cofilin / filament / cytoskeleton / STRUCTURAL PROTEIN
Function / homology
Function and homology information


cellular response to ether / cofilin-actin rod / positive regulation of protein localization to cell leading edge / positive regulation of establishment of cell polarity regulating cell shape / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / actin filament fragmentation / positive regulation of actin filament depolymerization ...cellular response to ether / cofilin-actin rod / positive regulation of protein localization to cell leading edge / positive regulation of establishment of cell polarity regulating cell shape / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / actin filament fragmentation / positive regulation of actin filament depolymerization / negative regulation of actin filament bundle assembly / positive regulation of embryonic development / modification of postsynaptic actin cytoskeleton / positive regulation of norepinephrine uptake / bBAF complex / GBAF complex / brahma complex / negative regulation of actin filament depolymerization / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / npBAF complex / nBAF complex / regulation of transepithelial transport / host-mediated activation of viral process / actin filament severing / Formation of the canonical BAF (cBAF) complex / morphogenesis of a polarized epithelium / negative regulation of cell adhesion / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / positive regulation of synaptic plasticity / Formation of the polybromo-BAF (pBAF) complex / Gap junction degradation / regulation of dendritic spine morphogenesis / protein localization to adherens junction / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / Cell-extracellular matrix interactions / establishment of spindle localization / regulation of G0 to G1 transition / dense body / RSC-type complex / Folding of actin by CCT/TriC / Tat protein binding / negative regulation of cell motility / actin filament depolymerization / RHO GTPases Activate ROCKs / postsynaptic actin cytoskeleton / cellular response to interleukin-6 / Regulation of CDH1 Function / apical protein localization / regulation of double-strand break repair / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / adherens junction assembly / RHOF GTPase cycle / regulation of nucleotide-excision repair / negative regulation of dendritic spine maintenance / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of cell motility / tight junction / SWI/SNF complex / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / positive regulation of T cell differentiation / cortical actin cytoskeleton / apical junction complex / cellular response to insulin-like growth factor stimulus / positive regulation of dendritic spine development / phosphatidylinositol bisphosphate binding / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / transporter regulator activity / positive regulation of proteolysis / positive regulation of double-strand break repair / Recycling pathway of L1 / cortical cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / establishment or maintenance of cell polarity / lamellipodium membrane / nitric-oxide synthase binding / mitotic cytokinesis / brush border / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / cellular response to interleukin-1 / positive regulation of focal adhesion assembly / regulation of synaptic vesicle endocytosis / negative regulation of cell differentiation / positive regulation of myoblast differentiation / RHO GTPases Activate WASPs and WAVEs / kinesin binding / positive regulation of lamellipodium assembly / regulation of protein localization to plasma membrane / postsynaptic density, intracellular component / RHO GTPases activate IQGAPs
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site ...ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Cofilin-1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsOosterheert W / Boiero Sanders M / Hofnagel O / Bieling P / Raunser S
Funding support Germany, European Union, 4 items
OrganizationGrant numberCountry
Max Planck Society Germany
Alexander von Humboldt Foundation Germany
German Research Foundation (DFG)BI 1998/2-1 Germany
European Research Council (ERC)856118European Union
CitationJournal: Cell / Year: 2025
Title: Choreography of rapid actin filament disassembly by coronin, cofilin, and AIP1.
Authors: Wout Oosterheert / Micaela Boiero Sanders / Oliver Hofnagel / Peter Bieling / Stefan Raunser /
Abstract: Rapid remodeling of actin filament (F-actin) networks is essential for the movement and morphogenesis of eukaryotic cells. The conserved actin-binding proteins coronin, cofilin, and actin-interacting ...Rapid remodeling of actin filament (F-actin) networks is essential for the movement and morphogenesis of eukaryotic cells. The conserved actin-binding proteins coronin, cofilin, and actin-interacting protein 1 (AIP1) act in synergy to promote rapid F-actin network disassembly, but the underlying mechanisms have remained elusive. Here, using cryo-electron microscopy (cryo-EM), we uncover the concerted molecular actions of coronin, cofilin, and AIP1 that lead to actin filament aging and severing. We find that the cooperative binding of coronin allosterically promotes inorganic phosphate release from F-actin and induces filament undertwisting, thereby priming the filament for cofilin binding. Cofilin then displaces coronin from the filament via a strand-restricted cooperative binding mechanism. The resulting cofilactin serves as a high-affinity platform for AIP1, which induces severing by acting as a clamp that disrupts inter-subunit filament contacts. In this "molecular squeezing" mechanism, AIP1 and not cofilin is responsible for filament severing. Our work redefines the role of key disassembly factors in actin dynamics.
History
DepositionMar 11, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53106.png

Downloads & links

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Map

FileDownload / File: emd_53106.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain, sharpened cryo-EM density map of the fully cofilin-1-decorated actin filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 600 pix.
= 408. Å		0.68 Å/pix.
x 600 pix.
= 408. Å		0.68 Å/pix.
x 600 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.114
Minimum - Maximum-0.3452586 - 0.89556074
Average (Standard dev.)0.000024365962 (±0.016966743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53106_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional unsharpened map of the fully cofilin-1-decorated actin...

Fileemd_53106_additional_1.map
AnnotationAdditional unsharpened map of the fully cofilin-1-decorated actin filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the fully cofilin-1-decorated actin filament

Fileemd_53106_half_map_1.map
AnnotationHalf map A of the fully cofilin-1-decorated actin filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the fully cofilin-1-decorated actin filament

Fileemd_53106_half_map_2.map
AnnotationHalf map B of the fully cofilin-1-decorated actin filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Beta-actin filament fully decorated by Cofilin-1.

EntireName: Beta-actin filament fully decorated by Cofilin-1.
Components
  • Complex: Beta-actin filament fully decorated by Cofilin-1.
    • Complex: Actin filament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Beta-actin filament fully decorated by Cofilin-1.

SupramoleculeName: Beta-actin filament fully decorated by Cofilin-1. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Actin filament

SupramoleculeName: Actin filament / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Assembled as a double stranded helix of beta-actin subunits.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Cofilin-1

SupramoleculeName: Cofilin-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Actin, cytoplasmic 1, N-terminally processed

MacromoleculeName: Actin, cytoplasmic 1, N-terminally processed / type: protein_or_peptide / ID: 1 / Details: actin filament / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.632422 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVT NWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGD GV THTVPIYEGY ...String:
DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVT NWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGD GV THTVPIYEGY ALPHAILRLD LAGRDLTDYL MKILTERGYS FTTTAEREIV RDIKEKLCYV ALDFEQEMAT AASSSSLE K SYELPDGQVI TIGNERFRCP EALFQPSFLG MESAGIHETT FNSIMKCDVD IRKDLYANTV LSGGTTMYPG IADRMQKEI TALAPSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI SKQEYDESGP SIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #2: Cofilin-1

MacromoleculeName: Cofilin-1 / type: protein_or_peptide / ID: 2 / Details: Cofilin / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.532531 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MASGVAVSDG VIKVFNDMKV RKSSTPEEVK KRKKAVLFCL SEDKKNIILE EGKEILVGDV GQTVDDPYAT FVKMLPDKDC RYALYDATY ETKESKKEDL VFIFWAPESA PLKSKMIYAS SKDAIKKKLT GIKHELQANC YEEVKDRCTL AEKLGGSAVI S LEGKPL

UniProtKB: Cofilin-1

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 7 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.1
Component:
ConcentrationNameFormula
10.0 mMHEPES
100.0 mMpotassium chlorideKCl
2.0 mMmagnesium chlorideMgCl2
1.0 mMEGTA
0.5 mMTCEP
0.02 % (v/v)Tween20

Details: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.02% Tween20).
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: The used Titan Krios G2 microscope contains an in-column Cs corrector.
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 14055 / Average electron dose: 65.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -162.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Software - details: Helical Refinement / Number images used: 798636
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Software - details: Patch CTF / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 10071093 / Software - Name: cryoSPARC (ver. 4.4) / Software - details: Filament tracer
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vao

Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6vao


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsPhenix real space refinement.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9qfd:
Cryo-EM structure of the fully cofilin-1-decorated actin filament (cofilactin)

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