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- EMDB-53118: Cryo-EM reconstruction of the cofilactin filament core bound by AIP1 -

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Basic information

Entry
Database: EMDB / ID: EMD-53118
TitleCryo-EM reconstruction of the cofilactin filament core bound by AIP1
Map dataDeepEMhancer-postprocessed (Wide target) density map of the cofilactin filament core bound by AIP1
Sample
  • Complex: Cofilactin filament core bound by AIP1
    • Complex: Actin filament
      • Protein or peptide: Cytoplasmic beta actin
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1
    • Complex: AIP1
      • Protein or peptide: AIP1
Keywordsactin / cofilin / filament / cytoskeleton / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.62 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 12, 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_53118.png

Downloads & links

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Map

FileDownload / File: emd_53118.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer-postprocessed (Wide target) density map of the cofilactin filament core bound by AIP1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 448 pix.
= 304.64 Å		0.68 Å/pix.
x 448 pix.
= 304.64 Å		0.68 Å/pix.
x 448 pix.
= 304.64 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: 0.215
Minimum - Maximum-0.0002571995 - 1.8371168
Average (Standard dev.)0.007821338 (±0.06534396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 304.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53118_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 cofilactin filament core...

Fileemd_53118_additional_1.map
AnnotationAdditional sharpened map of the cofilactin filament core bound by AIP1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional unsharpened map of the cofilactin filament core...

Fileemd_53118_additional_2.map
AnnotationAdditional unsharpened map of the cofilactin filament core bound by AIP1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the cofilactin filament core bound by AIP1

Fileemd_53118_half_map_1.map
AnnotationHalf map A of the cofilactin filament core bound by AIP1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the cofilactin filament core bound by AIP1

Fileemd_53118_half_map_2.map
AnnotationHalf map B of the cofilactin filament core bound by AIP1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cofilactin filament core bound by AIP1

EntireName: Cofilactin filament core bound by AIP1
Components
  • Complex: Cofilactin filament core bound by AIP1
    • Complex: Actin filament
      • Protein or peptide: Cytoplasmic beta actin
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1
    • Complex: AIP1
      • Protein or peptide: AIP1

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Supramolecule #1: Cofilactin filament core bound by AIP1

SupramoleculeName: Cofilactin filament core bound by AIP1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cofilin-1 and AIP1 bound to the actin filament
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
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Cofilin-1

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

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Supramolecule #4: AIP1

SupramoleculeName: AIP1 / 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 / 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: Cofilin-1

MacromoleculeName: Cofilin-1 / type: protein_or_peptide / ID: 2 / 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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Macromolecule #3: AIP1

MacromoleculeName: AIP1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAMGSMPYEI KKVFASLPQV ERGVSKIIGG DPKGNNFLYT NGKCVILRNI DNPALADIYT EHAHQVVVAK YAPSGFYIAS GDVSGKLRIW DTTQKEHLLK YEYQPFAGKI KDIAWTEDSK RIAVVGEGRE KFGAVFLWDS GSSVGEITGH NKVINSVDIK QSRPYRLATG ...String:
GAMGSMPYEI KKVFASLPQV ERGVSKIIGG DPKGNNFLYT NGKCVILRNI DNPALADIYT EHAHQVVVAK YAPSGFYIAS GDVSGKLRIW DTTQKEHLLK YEYQPFAGKI KDIAWTEDSK RIAVVGEGRE KFGAVFLWDS GSSVGEITGH NKVINSVDIK QSRPYRLATG SDDNCAAFFE GPPFKFKFTI GDHSRFVNCV RFSPDGNRFA TASADGQIYI YDGKTGEKVC ALGGSKAHDG GIYAISWSPD STHLLSASGD KTSKIWDVSV NSVVSTFPMG STVLDQQLGC LWQKDHLLSV SLSGYINYLD RNNPSKPLHV IKGHSKSIQC LTVHKNGGKS YIYSGSHDGH INYWDSETGE NDSFAGKGHT NQVSRMTVDE SGQLISCSMD DTVRYTSLML RDYSGQGVVK LDVQPKCVAV GPGGYAVVVC IGQIVLLKDQ RKCFSIDNPG YEPEVVAVHP GGDTVAIGGV DGNVRLYSIL GTTLKDEGKL LEAKGPVTDV AYSHDGAFLA VCDASKVVTV FSVADGYSEN NVFYGHHAKI VCLAWSPDNE HFASGGMDMM VYVWTLSDPE TRVKIQDAHR LHHVSSLAWL DEHTLVTTSH DASVKEWTIT YGTGGGGSGG GGSMDKDCEM KRTTLDSPLG KLELSGCEQG LHEIKLLGKG TSAADAVEVP APAAVLGGPE PLMQATAWLN AYFHQPEAIE EFPVPALHHP VFQQESFTRQ VLWKLLKVVK FGEVISYQQL AALAGNPAAT AAVKTALSGN PVPILIPCHR VVSSSGAVGG YEGGLAVKEW LLAHEGHRLG KPGLG

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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
0.015 % (v/v)Tween

Details: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.015% Tween)
GridModel: Quantifoil R2/1 / Material: GOLD / 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: 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) equipped with 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: 23082 / Average electron dose: 71.7 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: 8428096
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vao

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Software - details: Local Refinement / Number images used: 3643
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
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:

6vao


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe final model refinement was performed using Phenix real space refinement.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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