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- PDB-9qfw: Cryo-EM structure of the cofilactin barbed end bound by two AIP1 ... -

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Basic information

Entry
Database: PDB / ID: 9qfw
TitleCryo-EM structure of the cofilactin barbed end bound by two AIP1 molecules
Components
  • Actin, cytoplasmic 1, N-terminally processed
  • Cofilin-1
  • WD repeat-containing protein 1,Methylated-DNA--protein-cysteine methyltransferase
KeywordsSTRUCTURAL PROTEIN / actin / cofilin / AIP1 / barbed end / filament / cytoskeleton
Function / homology
Function and homology information


establishment of planar polarity of follicular epithelium / regulation of actin filament depolymerization / regulation of oligodendrocyte differentiation / 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 ...establishment of planar polarity of follicular epithelium / regulation of actin filament depolymerization / regulation of oligodendrocyte differentiation / 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 / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / actin filament fragmentation / maintenance of epithelial cell apical/basal polarity / positive regulation of actin filament depolymerization / negative regulation of actin filament bundle assembly / positive regulation of norepinephrine uptake / positive regulation of embryonic development / modification of postsynaptic actin cytoskeleton / DNA-methyltransferase activity / negative regulation of actin filament depolymerization / Formation of the embryonic stem cell BAF (esBAF) complex / bBAF complex / neutrophil migration / cellular response to cytochalasin B / cortical cytoskeleton organization / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / regulation of transepithelial transport / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / actin filament severing / apical junction assembly / Formation of the polybromo-BAF (pBAF) complex / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / host-mediated activation of viral process / Formation of the non-canonical BAF (ncBAF) complex / Gap junction degradation / GBAF complex / regulation of dendritic spine morphogenesis / Cell-extracellular matrix interactions / regulation of G0 to G1 transition / protein localization to adherens junction / positive regulation of synaptic plasticity / establishment of spindle localization / dense body / negative regulation of cell adhesion / DNA alkylation repair / Folding of actin by CCT/TriC / Tat protein binding / regulation of ventricular cardiac muscle cell membrane repolarization / negative regulation of cell motility / actin filament depolymerization / negative regulation of cell size / postsynaptic actin cytoskeleton / RHO GTPases Activate ROCKs / RSC-type complex / Regulation of CDH1 Function / cellular response to interleukin-6 / neutrophil mediated immunity / regulation of double-strand break repair / regulation of nucleotide-excision repair / podosome / Prefoldin mediated transfer of substrate to CCT/TriC / regulation of cell morphogenesis / Adherens junctions interactions / RHOF GTPase cycle / cell projection organization / adherens junction assembly / locomotion / negative regulation of dendritic spine maintenance / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / platelet formation / Interaction between L1 and Ankyrins / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of cell motility / tight junction / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / neural crest cell migration / sarcomere organization / phosphatidylinositol bisphosphate binding / apical junction complex / cortical actin cytoskeleton / cellular response to insulin-like growth factor stimulus / positive regulation of double-strand break repair / regulation of norepinephrine uptake / transporter regulator activity / maintenance of blood-brain barrier / establishment of cell polarity / positive regulation of dendritic spine development
Similarity search - Function
Nitrous oxide reductase, N-terminal / 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 ...Nitrous oxide reductase, N-terminal / 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 / G-protein beta WD-40 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 / WD repeat-containing protein 1 / Methylated-DNA--protein-cysteine methyltransferase / Cofilin-1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 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 12, 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: Cofilin-1
G: Cofilin-1
H: Cofilin-1
I: Cofilin-1
J: Cofilin-1
P: WD repeat-containing protein 1,Methylated-DNA--protein-cysteine methyltransferase
Q: WD repeat-containing protein 1,Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)476,60422
Polymers474,34712
Non-polymers2,25810
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.: 5 / 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.: 5
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 WD repeat-containing protein 1,Methylated-DNA--protein-cysteine methyltransferase / Actin-interacting protein 1 / AIP1 / NORI-1 / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6- ...Actin-interacting protein 1 / AIP1 / NORI-1 / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 86760.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: AIP1 has a C-terminal SNAP tag,AIP1 has a C-terminal SNAP tag
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR1, MGMT / Cell line (production host): BTI-Tnao38 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: O75083, UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
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
IDNameTypeDetailsEntity IDParent-IDSource
1Cofilactin barbed end bound by two AIP1 moleculesCOMPLEXBarbed end of the actin filament fully decorated by Cofilin-1 and bound by two AIP1 molecules#1-#30MULTIPLE SOURCES
2Actin filamentCOMPLEX#11RECOMBINANT
3Cofilin-1COMPLEX#21RECOMBINANT
4AIP1COMPLEX#31RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22NO
31NO
44
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Trichoplusia ni (cabbage looper)7111
22Trichoplusia ni (cabbage looper)7111
33Escherichia coli BL21(DE3) (bacteria)469008
44Trichoplusia ni (cabbage looper)7111
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, 0.015% Tween20)
Buffer component
IDConc.NameBuffer-ID
110 mMHEPES1
2100 mMpotassium chloride1
32 mMmagnesium chloride1
41 mMEGTA1
50.5 mMTCEP1
60.015 % (v/v)Tween201
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / 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 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: 71.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 23082
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV
Spherical aberration corrector: Data were collected using a 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) equipped with an in-column Cs corrector

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Processing

EM software
IDNameVersionCategoryDetails
1crYOLO1.9particle selection
2EPUimage acquisition
4cryoSPARC4.4CTF correctionPatch CTF
7UCSF ChimeraX1.8model fitting
8Coot0.9.8.1model fitting
10PHENIX1.21rc1_5015model refinement
11cryoSPARC4.4initial Euler assignment
12cryoSPARC4.4final Euler assignment
13cryoSPARC4.4classification
14cryoSPARC4.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3916837
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23577 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: Phenix real space refinement
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
19QFJ

9qfj

19QFJ1PDBexperimental model
21O750832AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 106.48 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002130386
ELECTRON MICROSCOPYf_angle_d0.503441135
ELECTRON MICROSCOPYf_chiral_restr0.04434579
ELECTRON MICROSCOPYf_plane_restr0.00335237
ELECTRON MICROSCOPYf_dihedral_angle_d8.47724159

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