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- PDB-9qfk: Cryo-EM structure of the Coronin-1B-decorated actin filament boun... -

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Basic information

Entry
Database: PDB / ID: 9qfk
TitleCryo-EM structure of the Coronin-1B-decorated actin filament bound by one Cofilin-1 molecule (crosslinked)
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 / MGMT-mediated DNA damage reversal / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping / neural fold formation / negative regulation of lamellipodium assembly ...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 / MGMT-mediated DNA damage reversal / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping / neural fold formation / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / protein localization to cell leading edge / actin filament fragmentation / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / Arp2/3 complex binding / negative regulation of smooth muscle cell chemotaxis / positive regulation of actin filament depolymerization / negative regulation of actin filament bundle assembly / negative regulation of Arp2/3 complex-mediated actin nucleation / modification of postsynaptic actin cytoskeleton / positive regulation of embryonic development / positive regulation of norepinephrine uptake / regulation of Arp2/3 complex-mediated actin nucleation / Regulation of CDH1 Function / positive regulation of synaptic plasticity / Formation of the polybromo-BAF (pBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / Formation of the canonical BAF (cBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / DNA-methyltransferase activity / endothelial cell chemotaxis / negative regulation of actin filament depolymerization / bBAF complex / cellular response to cytochalasin B / npBAF complex / nBAF complex / brahma complex / actin filament severing / regulation of transepithelial transport / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of dendritic spine morphogenesis / structural constituent of postsynaptic actin cytoskeleton / host-mediated activation of viral process / GBAF complex / Gap junction degradation / Folding of actin by CCT/TriC / regulation of G0 to G1 transition / Cell-extracellular matrix interactions / protein localization to adherens junction / establishment of spindle localization / cell projection organization / actin filament depolymerization / dense body / negative regulation of cell adhesion / DNA alkylation repair / Tat protein binding / negative regulation of cell motility / ruffle organization / postsynaptic actin cytoskeleton / RHO GTPases Activate ROCKs / Prefoldin mediated transfer of substrate to CCT/TriC / negative regulation of cell size / RSC-type complex / cellular response to interleukin-6 / regulation of double-strand break repair / regulation of nucleotide-excision repair / regulation of cell morphogenesis / Adherens junctions interactions / negative regulation of dendritic spine maintenance / positive regulation of lamellipodium morphogenesis / RHOF GTPase cycle / adherens junction assembly / apical protein localization / Sensory processing of sound by inner hair cells of the cochlea / Sensory processing of sound by outer hair cells of the cochlea / neural crest cell migration / Interaction between L1 and Ankyrins / tight junction / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of cell motility / positive regulation of T cell differentiation / phosphatidylinositol bisphosphate binding / apical junction complex / cellular response to insulin-like growth factor stimulus / cortical actin cytoskeleton / positive regulation of double-strand break repair / maintenance of blood-brain barrier / regulation of norepinephrine uptake / transporter regulator activity / nitric-oxide synthase binding / positive regulation of dendritic spine development / establishment of cell polarity / cortical cytoskeleton / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex
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. / ADF/Cofilin / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / 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: 3.99 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: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
I: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
J: Cofilin-1
K: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
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)761,84928
Polymers758,68814
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
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.: 6
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
#3: Protein Cofilin-1 / 18 kDa phosphoprotein / p18 / Cofilin / non-muscle isoform


Mass: 18532.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cofilin-1 with disordered N-terminus / Source: (gene. exp.) Homo sapiens (human) / Gene: CFL1, CFL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23528
#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
1Cryo-EM structure of the Coronin-1B-decorated actin filament bound by one Cofilin-1 molecule (crosslinked)COMPLEX#1-#30MULTIPLE SOURCES
2Actin filamentCOMPLEX#11RECOMBINANTAssembled as a double stranded helix of beta-actin subunits.
3Coronin-1BCOMPLEX#21RECOMBINANT
4Cofilin-1COMPLEX#31RECOMBINANT
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: 62.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 22906
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
1cryoSPARC4.3.1particle selectionFilament tracer
2EPUimage acquisition
4cryoSPARC4.3.1CTF correctionPatch CTF
7Coot0.9.8.1model fitting
8UCSF ChimeraX1.8model fitting
10cryoSPARC4.3.1initial Euler assignment
11cryoSPARC4.3.1final Euler assignment
12cryoSPARC4.3.1classification
13cryoSPARC4.3.13D reconstructionLocal Refinement
14PHENIX1.21rc1_5015model refinement
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8030748
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9374 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: Phenix real space refinement.
Atomic model buildingPDB-ID: 9QFB

9qfb


Accession code: 9QFB / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 251.97 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00240939
ELECTRON MICROSCOPYf_angle_d0.588355593
ELECTRON MICROSCOPYf_chiral_restr0.04296167
ELECTRON MICROSCOPYf_plane_restr0.00337157
ELECTRON MICROSCOPYf_dihedral_angle_d6.39525602

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