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Entry
Database: EMDB / ID: EMD-53107
TitleCryo-EM structure of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on separate actin strands
Map dataMain, sharpened cryo-EM density map of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on separate actin strands
Sample
  • Complex: Beta-actin filament hetero-decorated by Coronin-1B and Cofilin-1.
    • Complex: Actin filament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Complex: Coronin-1B
      • Protein or peptide: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsactin / coronin / cofilin / filament / cytoskeleton / STRUCTURAL PROTEIN
Function / homology
Function and homology information


actin filament branching / MGMT-mediated DNA damage reversal / 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 ...actin filament branching / MGMT-mediated DNA damage reversal / 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 / protein localization to cell leading edge / negative regulation of postsynaptic density organization / actin filament fragmentation / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / Arp2/3 complex binding / positive regulation of actin filament depolymerization / negative regulation of smooth muscle cell chemotaxis / regulation of Arp2/3 complex-mediated actin nucleation / modification of postsynaptic actin cytoskeleton / positive regulation of norepinephrine uptake / positive regulation of embryonic development / DNA-methyltransferase activity / negative regulation of actin filament bundle assembly / negative regulation of Arp2/3 complex-mediated actin nucleation / positive regulation of synaptic plasticity / 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 / Formation of annular gap junctions / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / regulation of dendritic spine morphogenesis / protein localization to adherens junction / establishment of spindle localization / host-mediated activation of viral process / actin filament depolymerization / dense body / cell projection organization / postsynaptic actin cytoskeleton / Tat protein binding / ruffle organization / negative regulation of cell adhesion / negative regulation of cell motility / DNA alkylation repair / RHO GTPases Activate ROCKs / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / negative regulation of cell size / regulation of double-strand break repair / regulation of nucleotide-excision repair / cellular response to interleukin-6 / regulation of cell morphogenesis / Adherens junctions interactions / negative regulation of dendritic spine maintenance / RHOF GTPase cycle / adherens junction assembly / positive regulation of lamellipodium morphogenesis / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / neural crest cell migration / Interaction between L1 and Ankyrins / tight junction / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of cell motility / positive regulation of T cell differentiation / apical junction complex / cortical actin cytoskeleton / phosphatidylinositol bisphosphate binding / cellular response to insulin-like growth factor stimulus / regulation of norepinephrine uptake / positive regulation of double-strand break repair / transporter regulator activity / maintenance of blood-brain barrier / establishment of cell polarity / nitric-oxide synthase binding / positive regulation of dendritic spine development / cortical cytoskeleton / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / cell leading edge / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / brush border / regulation of G1/S transition of mitotic cell cycle
Similarity search - Function
Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / ADF/Cofilin / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily ...Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / ADF/Cofilin / 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 / 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 / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Methylated-DNA--protein-cysteine methyltransferase / Cofilin-1 / Actin, cytoplasmic 1 / Coronin-1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 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: To Be Published
Title: Choreography of rapid actin filament disassembly by coronin, cofilin and AIP1
Authors: Oosterheert W / Boiero Sanders M / Hofnagel O / Bieling P / Raunser S
History
DepositionMar 11, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53107.png

Downloads & links

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Map

FileDownload / File: emd_53107.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain, sharpened cryo-EM density map of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on separate actin strands
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: 0.0329
Minimum - Maximum-0.10507203 - 0.18655688
Average (Standard dev.)0.00010262156 (±0.005965612)
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_53107_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 actin filament hetero-decorated...

Fileemd_53107_additional_1.map
AnnotationAdditional unsharpened map of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on separate actin strands
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the actin filament hetero-decorated...

Fileemd_53107_half_map_1.map
AnnotationHalf map A of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on separate actin strands
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the actin filament hetero-decorated...

Fileemd_53107_half_map_2.map
AnnotationHalf map B of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on separate actin strands
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 hetero-decorated by Coronin-1B and Cofilin-1.

EntireName: Beta-actin filament hetero-decorated by Coronin-1B and Cofilin-1.
Components
  • Complex: Beta-actin filament hetero-decorated by Coronin-1B and Cofilin-1.
    • Complex: Actin filament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Complex: Coronin-1B
      • Protein or peptide: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Beta-actin filament hetero-decorated by Coronin-1B and Cofilin-1.

SupramoleculeName: Beta-actin filament hetero-decorated by Coronin-1B and Cofilin-1.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: #3
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: #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 / 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 / Number of copies: 4 / 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: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase

MacromoleculeName: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
EC number: methylated-DNA-[protein]-cysteine S-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.788086 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAMGSMSFRK VVRQSKFRHV FGQPVKNDQC YEDIRVSRVT WDSTFCAVNP KFLAVIVEAS GGGAFLVLPL SKTGRIDKAY PTVCGHTGP VLDIDWCPHN DEVIASGSED CTVMVWQIPE NGLTSPLTEP VVVLEGHTKR VGIIAWHPTA RNVLLSAGCD N VVLIWNVG ...String:
GAMGSMSFRK VVRQSKFRHV FGQPVKNDQC YEDIRVSRVT WDSTFCAVNP KFLAVIVEAS GGGAFLVLPL SKTGRIDKAY PTVCGHTGP VLDIDWCPHN DEVIASGSED CTVMVWQIPE NGLTSPLTEP VVVLEGHTKR VGIIAWHPTA RNVLLSAGCD N VVLIWNVG TAEELYRLDS LHPDLIYNVS WNHNGSLFCS ACKDKSVRII DPRRGTLVAE REKAHEGARP MRAIFLADGK VF TTGFSRM SERQLALWDP ENLEEPMALQ ELDSSNGALL PFYDPDTSVV YVCGKGDSSI RYFEITEEPP YIHFLNTFTS KEP QRGMGS MPKRGLEVSK CEIARFYKLH ERKCEPIVMT VPRKSDLFQD DLYPDTAGPE AALEAEEWVS GRDADPILIS LREA YVPSK QRDLKISRRN VLSDSRPAMA PGSSHLGAPA STTTAADATP SGSLARAGEA GKLEEVMQEL RALRALVKEQ GDRIC RLEE QLGRMENGDA GTGGGGSGGG GSMDKDCEMK RTTLDSPLGK LELSGCEQGL HEIKLLGKGT SAADAVEVPA PAAVLG GPE PLMQATAWLN AYFHQPEAIE EFPVPALHHP VFQQESFTRQ VLWKLLKVVK FGEVISYQQL AALAGNPAAT AAVKTAL SG NPVPILIPCH RVVSSSGAVG GYEGGLAVKE WLLAHEGHRL GKPGLG

UniProtKB: Coronin-1B, Methylated-DNA--protein-cysteine methyltransferase

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / 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 #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / 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
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: 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

Particle selectionNumber selected: 10071093
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Software - details: Patch CTF / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

53096

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Software - details: Helical Refinement / Number images used: 40453
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4) / Details: CryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9qf2


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

PDB-9qfe:
Cryo-EM structure of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on separate actin strands

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