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- EMDB-53112: Cryo-EM reconstruction of the Coronin-1B-decorated actin filament... -

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Basic information

Entry
Database: EMDB / ID: EMD-53112
TitleCryo-EM reconstruction of the Coronin-1B-decorated actin filament bound by three Cofilin-1 molecules (crosslinked)
Map dataMain, unsharpened cryo-EM density map of the Coronin-1B-decorated actin filament bound by three Cofilin-1 molecules (crosslinked)
Sample
  • Complex: Cryo-EM structure of the Coronin-1B-decorated actin filament bound by three Cofilin-1 molecules (crosslinked)
    • Complex: Actin filament
      • Protein or peptide: Cytoplasmic beta actin
    • Complex: Coronin-1B
      • Protein or peptide: Coronin-1B
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1
Keywordsactin / coronin / cofilin / filament / cytoskeleton / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.36 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-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53112.png

Downloads & links

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Map

FileDownload / File: emd_53112.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain, unsharpened cryo-EM density map of the Coronin-1B-decorated actin filament bound by three Cofilin-1 molecules (crosslinked)
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: 0.14
Minimum - Maximum-0.13296433 - 0.49093196
Average (Standard dev.)0.001561146 (±0.02793048)
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_53112_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional sharpened map of the Coronin-1B-decorated actin filament...

Fileemd_53112_additional_1.map
AnnotationAdditional sharpened map of the Coronin-1B-decorated actin filament bound by three Cofilin-1 molecules (crosslinked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the Coronin-1B-decorated actin filament...

Fileemd_53112_half_map_1.map
AnnotationHalf map B of the Coronin-1B-decorated actin filament bound by three Cofilin-1 molecules (crosslinked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the Coronin-1B-decorated actin filament...

Fileemd_53112_half_map_2.map
AnnotationHalf map A of the Coronin-1B-decorated actin filament bound by three Cofilin-1 molecules (crosslinked)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the Coronin-1B-decorated actin filament boun...

EntireName: Cryo-EM structure of the Coronin-1B-decorated actin filament bound by three Cofilin-1 molecules (crosslinked)
Components
  • Complex: Cryo-EM structure of the Coronin-1B-decorated actin filament bound by three Cofilin-1 molecules (crosslinked)
    • Complex: Actin filament
      • Protein or peptide: Cytoplasmic beta actin
    • Complex: Coronin-1B
      • Protein or peptide: Coronin-1B
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1

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Supramolecule #1: Cryo-EM structure of the Coronin-1B-decorated actin filament boun...

SupramoleculeName: Cryo-EM structure of the Coronin-1B-decorated actin filament bound by three Cofilin-1 molecules (crosslinked)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: Coronin-1B

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

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Supramolecule #4: Cofilin-1

SupramoleculeName: Cofilin-1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cytoplasmic beta actin

MacromoleculeName: Cytoplasmic beta actin / type: protein_or_peptide / ID: 1 / Details: Actin filament / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVTNWDD MEKIWHHTFY NELRVAPEEH PVLLTEAPLN PKANREKMTQ IMFETFNTPA MYVAIQAVLS LYASGRTTGI VMDSGDGVTH TVPIYEGYAL ...String:
DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVTNWDD MEKIWHHTFY NELRVAPEEH PVLLTEAPLN PKANREKMTQ IMFETFNTPA MYVAIQAVLS LYASGRTTGI VMDSGDGVTH TVPIYEGYAL PHAILRLDLA GRDLTDYLMK ILTERGYSFT TTAEREIVRD IKEKLCYVAL DFEQEMATAA SSSSLEKSYE LPDGQVITIG NERFRCPEAL FQPSFLGMES AGIHETTFNS IMKCDVDIRK DLYANTVLSG GTTMYPGIAD RMQKEITALA PSTMKIKIIA PPERKYSVWI GGSILASLST FQQMWISKQE YDESGPSIVH RKCF

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Macromolecule #2: Coronin-1B

MacromoleculeName: Coronin-1B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: GAMGSMSFRK VVRQSKFRHV FGQPVKNDQC YEDIRVSRVT WDSTFCAVNP KFLAVIVEAS GGGAFLVLPL SKTGRIDKAY PTVCGHTGPV LDIDWCPHND EVIASGSEDC TVMVWQIPEN GLTSPLTEPV VVLEGHTKRV GIIAWHPTAR NVLLSAGCDN VVLIWNVGTA ...String:
GAMGSMSFRK VVRQSKFRHV FGQPVKNDQC YEDIRVSRVT WDSTFCAVNP KFLAVIVEAS GGGAFLVLPL SKTGRIDKAY PTVCGHTGPV LDIDWCPHND EVIASGSEDC TVMVWQIPEN GLTSPLTEPV VVLEGHTKRV GIIAWHPTAR NVLLSAGCDN VVLIWNVGTA EELYRLDSLH PDLIYNVSWN HNGSLFCSAC KDKSVRIIDP RRGTLVAERE KAHEGARPMR AIFLADGKVF TTGFSRMSER QLALWDPENL EEPMALQELD SSNGALLPFY DPDTSVVYVC GKGDSSIRYF EITEEPPYIH FLNTFTSKEP QRGMGSMPKR GLEVSKCEIA RFYKLHERKC EPIVMTVPRK SDLFQDDLYP DTAGPEAALE AEEWVSGRDA DPILISLREA YVPSKQRDLK ISRRNVLSDS RPAMAPGSSH LGAPASTTTA ADATPSGSLA RAGEAGKLEE VMQELRALRA LVKEQGDRIC RLEEQLGRME NGDAGTGGGG SGGGGSMDKD CEMKRTTLDS PLGKLELSGC EQGLHEIKLL GKGTSAADAV EVPAPAAVLG GPEPLMQATA WLNAYFHQPE AIEEFPVPAL HHPVFQQESF TRQVLWKLLK VVKFGEVISY QQLAALAGNP AATAAVKTAL SGNPVPILIP CHRVVSSSGA VGGYEGGLAV KEWLLAHEGH RLGKPGLG

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Macromolecule #3: Cofilin-1

MacromoleculeName: Cofilin-1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MASGVAVSDG VIKVFNDMKV RKSSTPEEVK KRKKAVLFCL SEDKKNIILE EGKEILVGDV GQTVDDPYAT FVKMLPDKDC RYALYDATYE TKESKKEDLV FIFWAPESAP LKSKMIYASS KDAIKKKLTG IKHELQANCY EEVKDRCTLA EKLGGSAVIS LEGKPL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle 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: 10 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: 22906 / Average electron dose: 62.3 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

Particle selectionNumber selected: 8030748
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1) / Software - details: Patch CTF / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

53105

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Software - details: Local Refinement / Number images used: 5537
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1) / Details: CryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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