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- PDB-9qfe: Cryo-EM structure of the actin filament hetero-decorated by Coron... -

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Basic information

Entry
Database: PDB / ID: 9qfe
TitleCryo-EM structure of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on separate actin strands
Components
  • Actin, cytoplasmic 1, N-terminally processed
  • Cofilin-1
  • Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
KeywordsSTRUCTURAL PROTEIN / actin / coronin / cofilin / filament / cytoskeleton
Function / homology
Function and homology information


actin filament branching / 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 / neural fold formation / negative regulation of lamellipodium assembly / MGMT-mediated DNA damage reversal ...actin filament branching / 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 / neural fold formation / negative regulation of lamellipodium assembly / MGMT-mediated DNA damage reversal / negative regulation of postsynaptic density organization / protein localization to cell leading edge / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / actin filament fragmentation / Arp2/3 complex binding / negative regulation of smooth muscle cell chemotaxis / positive regulation of actin filament depolymerization / negative regulation of actin filament bundle assembly / regulation of Arp2/3 complex-mediated actin nucleation / positive regulation of embryonic development / modification of postsynaptic actin cytoskeleton / positive regulation of norepinephrine uptake / endothelial cell chemotaxis / negative regulation of Arp2/3 complex-mediated actin nucleation / DNA-methyltransferase activity / negative regulation of actin filament depolymerization / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / bBAF complex / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / actin filament severing / regulation of transepithelial transport / host-mediated activation of viral process / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / ruffle organization / morphogenesis of a polarized epithelium / Formation of the polybromo-BAF (pBAF) complex / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / positive regulation of synaptic plasticity / regulation of dendritic spine morphogenesis / Gap junction degradation / establishment of spindle localization / Formation of the non-canonical BAF (ncBAF) complex / GBAF complex / protein localization to adherens junction / regulation of G0 to G1 transition / Cell-extracellular matrix interactions / negative regulation of cell adhesion / DNA alkylation repair / dense body / negative regulation of cell motility / Folding of actin by CCT/TriC / Tat protein binding / actin filament depolymerization / RHO GTPases Activate ROCKs / postsynaptic actin cytoskeleton / negative regulation of cell size / RSC-type complex / cellular response to interleukin-6 / Regulation of CDH1 Function / regulation of double-strand break repair / regulation of cell morphogenesis / regulation of nucleotide-excision repair / positive regulation of lamellipodium morphogenesis / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / cell projection organization / apical protein localization / negative regulation of dendritic spine maintenance / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / positive regulation of cell motility / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / tight junction / Sensory processing of sound by inner hair cells of the cochlea / neural crest cell migration / positive regulation of T cell differentiation / cortical actin cytoskeleton / apical junction complex / phosphatidylinositol bisphosphate binding / cellular response to insulin-like growth factor stimulus / positive regulation of double-strand break repair / establishment of cell polarity / maintenance of blood-brain barrier / positive regulation of dendritic spine development / regulation of norepinephrine uptake / transporter regulator activity / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / cell leading edge / establishment or maintenance of cell polarity
Similarity search - Function
Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site ...Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / 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 / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Methylated-DNA--protein-cysteine methyltransferase / Cofilin-1 / Actin, cytoplasmic 1 / Coronin-1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsOosterheert, W. / Boiero Sanders, M. / Hofnagel, O. / Bieling, P. / Raunser, S.
Funding support Germany, European Union, 4items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Dec 10, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _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, cytoplasmic 1, N-terminally processed
B: Actin, cytoplasmic 1, N-terminally processed
C: Actin, cytoplasmic 1, N-terminally processed
D: Actin, cytoplasmic 1, N-terminally processed
E: Actin, cytoplasmic 1, N-terminally processed
F: Actin, cytoplasmic 1, N-terminally processed
G: Actin, cytoplasmic 1, N-terminally processed
H: Cofilin-1
I: Cofilin-1
J: Cofilin-1
K: Cofilin-1
L: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
M: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
N: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)593,08228
Polymers589,92114
Non-polymers3,16114
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

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


Mass: 41632.422 Da / Num. of mol.: 7 / Mutation: C272A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Cell line (production host): BTI-Tnao38 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60709
#2: Protein
Cofilin-1 / 18 kDa phosphoprotein / p18 / Cofilin / non-muscle isoform


Mass: 18532.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFL1, CFL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23528
#3: Protein Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase / Coronin-2 / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 74788.086 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CORO1B, MGMT / Cell line (production host): BTI-Tnao38 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9BR76, UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails (eV)
1Beta-actin filament hetero-decorated by Coronin-1B and Cofilin-1.COMPLEX#1-#30RECOMBINANT
2Actin filamentCOMPLEX#11RECOMBINANTAssembled as a double stranded helix of beta-actin subunits.
3Coronin-1BCOMPLEX#31RECOMBINANT
4Cofilin-1COMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33
44
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Trichoplusia ni (cabbage looper)7111BTI-Tnao38
32Trichoplusia ni (cabbage looper)7111BTI-Tnao38
43Trichoplusia ni (cabbage looper)7111BTI-Tnao38
54Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.1
Details: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.02% Tween20).
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES1
2100 mMpotassium chlorideKCl1
32 mMmagnesium chlorideMgCl21
41 mMEGTA1
50.5 mMTCEP1
60.02 % (v/v)Tween201
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 286 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: 105000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1200 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 65.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14055
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV
Spherical aberration corrector: The used Titan Krios G2 microscope contains an in-column Cs corrector.

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.4particle selectionFilament tracer
2EPUimage acquisition
4cryoSPARC4.4CTF correctionPatch CTF
7Coot0.9.8.1model fitting
8UCSF ChimeraX1.8model fitting
10PHENIX1.21rc1_5015model refinement
11cryoSPARC4.4initial Euler assignment
12cryoSPARC4.4final Euler assignment
13cryoSPARC4.4classification
14cryoSPARC4.43D reconstructionHelical Refinement
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10071093
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40453 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: Phenix real space refinement.
Atomic model buildingPDB-ID: 9QF2

9qf2


Accession code: 9QF2 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 73.31 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002135166
ELECTRON MICROSCOPYf_angle_d0.483647676
ELECTRON MICROSCOPYf_chiral_restr0.04315315
ELECTRON MICROSCOPYf_plane_restr0.00326100
ELECTRON MICROSCOPYf_dihedral_angle_d8.89094823

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