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- EMDB-53122: Cryo-EM structure of the cofilactin barbed end bound by two AIP1 ... -

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Entry
Database: EMDB / ID: EMD-53122
TitleCryo-EM structure of the cofilactin barbed end bound by two AIP1 molecules
Map dataMain, sharpened cryo-EM density map of the cofilactin barbed end bound by two AIP1 molecules
Sample
  • Complex: Cofilactin barbed end bound by two AIP1 molecules
    • Complex: Actin filament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1
    • Complex: AIP1
      • Protein or peptide: WD repeat-containing protein 1,Methylated-DNA--protein-cysteine methyltransferase
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsactin / cofilin / AIP1 / barbed end / filament / cytoskeleton / STRUCTURAL PROTEIN
Function / homology
Function and homology information


establishment of planar polarity of follicular epithelium / regulation of actin filament depolymerization / regulation of oligodendrocyte differentiation / 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 ...establishment of planar polarity of follicular epithelium / regulation of actin filament depolymerization / regulation of oligodendrocyte differentiation / 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 / negative regulation of postsynaptic density organization / actin filament fragmentation / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / maintenance of epithelial cell apical/basal polarity / positive regulation of actin filament depolymerization / 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 / positive regulation of synaptic plasticity / negative regulation of actin filament depolymerization / bBAF complex / cellular response to cytochalasin B / npBAF complex / neutrophil migration / cortical cytoskeleton organization / 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 / apical junction assembly / 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 / regulation of ventricular cardiac muscle cell membrane repolarization / 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 / locomotion / negative regulation of cell size / regulation of double-strand break repair / regulation of nucleotide-excision repair / cellular response to interleukin-6 / neutrophil mediated immunity / regulation of cell morphogenesis / Adherens junctions interactions / negative regulation of dendritic spine maintenance / RHOF GTPase cycle / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / neural crest cell migration / Interaction between L1 and Ankyrins / podosome / tight junction / platelet formation / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / sarcomere organization / 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 / Regulation of MITF-M-dependent genes involved in pigmentation
Similarity search - Function
Nitrous oxide reductase, N-terminal / 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 ...Nitrous oxide reductase, N-terminal / 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 / 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 / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD repeat-containing protein 1 / Methylated-DNA--protein-cysteine methyltransferase / Cofilin-1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 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_53122.png

Downloads & links

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Map

FileDownload / File: emd_53122.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain, sharpened cryo-EM density map of the cofilactin barbed end bound by two AIP1 molecules
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: 0.0482
Minimum - Maximum-0.1401241 - 0.28104705
Average (Standard dev.)0.000067920584 (±0.0074948287)
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_53122_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 cofilactin barbed end...

Fileemd_53122_additional_1.map
AnnotationAdditional unsharpened map of the cofilactin barbed end bound by two AIP1 molecules
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 barbed end bound by two AIP1 molecules

Fileemd_53122_half_map_1.map
AnnotationHalf map B of the cofilactin barbed end bound by two AIP1 molecules
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 barbed end bound by two AIP1 molecules

Fileemd_53122_half_map_2.map
AnnotationHalf map A of the cofilactin barbed end bound by two AIP1 molecules
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 barbed end bound by two AIP1 molecules

EntireName: Cofilactin barbed end bound by two AIP1 molecules
Components
  • Complex: Cofilactin barbed end bound by two AIP1 molecules
    • Complex: Actin filament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Complex: Cofilin-1
      • Protein or peptide: Cofilin-1
    • Complex: AIP1
      • Protein or peptide: WD repeat-containing protein 1,Methylated-DNA--protein-cysteine methyltransferase
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Cofilactin barbed end bound by two AIP1 molecules

SupramoleculeName: Cofilactin barbed end bound by two AIP1 molecules / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Barbed end of the actin filament fully decorated by Cofilin-1 and bound by two AIP1 molecules
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: Actin, cytoplasmic 1, N-terminally processed

MacromoleculeName: Actin, cytoplasmic 1, N-terminally processed / type: protein_or_peptide / ID: 1 / Number of copies: 5 / 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: 5 / 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: WD repeat-containing protein 1,Methylated-DNA--protein-cysteine m...

MacromoleculeName: WD repeat-containing protein 1,Methylated-DNA--protein-cysteine methyltransferase
type: protein_or_peptide / ID: 3
Details: AIP1 has a C-terminal SNAP tag,AIP1 has a C-terminal SNAP tag
Number of copies: 2 / Enantiomer: LEVO
EC number: methylated-DNA-[protein]-cysteine S-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.760906 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAMGSMPYEI KKVFASLPQV ERGVSKIIGG DPKGNNFLYT NGKCVILRNI DNPALADIYT EHAHQVVVAK YAPSGFYIAS GDVSGKLRI WDTTQKEHLL KYEYQPFAGK IKDIAWTEDS KRIAVVGEGR EKFGAVFLWD SGSSVGEITG HNKVINSVDI K QSRPYRLA ...String:
GAMGSMPYEI KKVFASLPQV ERGVSKIIGG DPKGNNFLYT NGKCVILRNI DNPALADIYT EHAHQVVVAK YAPSGFYIAS GDVSGKLRI WDTTQKEHLL KYEYQPFAGK IKDIAWTEDS KRIAVVGEGR EKFGAVFLWD SGSSVGEITG HNKVINSVDI K QSRPYRLA TGSDDNCAAF FEGPPFKFKF TIGDHSRFVN CVRFSPDGNR FATASADGQI YIYDGKTGEK VCALGGSKAH DG GIYAISW SPDSTHLLSA SGDKTSKIWD VSVNSVVSTF PMGSTVLDQQ LGCLWQKDHL LSVSLSGYIN YLDRNNPSKP LHV IKGHSK SIQCLTVHKN GGKSYIYSGS HDGHINYWDS ETGENDSFAG KGHTNQVSRM TVDESGQLIS CSMDDTVRYT SLML RDYSG QGVVKLDVQP KCVAVGPGGY AVVVCIGQIV LLKDQRKCFS IDNPGYEPEV VAVHPGGDTV AIGGVDGNVR LYSIL GTTL KDEGKLLEAK GPVTDVAYSH DGAFLAVCDA SKVVTVFSVA DGYSENNVFY GHHAKIVCLA WSPDNEHFAS GGMDMM VYV WTLSDPETRV KIQDAHRLHH VSSLAWLDEH TLVTTSHDAS VKEWTITYGT GGGGSGGGGS MDKDCEMKRT TLDSPLG KL ELSGCEQGLH EIKLLGKGTS AADAVEVPAP AAVLGGPEPL MQATAWLNAY FHQPEAIEEF PVPALHHPVF QQESFTRQ V LWKLLKVVKF GEVISYQQLA ALAGNPAATA AVKTALSGNP VPILIPCHRV VSSSGAVGGY EGGLAVKEWL LAHEGHRLG KPGLG

UniProtKB: WD repeat-containing protein 1, Methylated-DNA--protein-cysteine methyltransferase

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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:
ConcentrationName
10.0 mMHEPES
100.0 mMpotassium chloride
2.0 mMmagnesium chloride
1.0 mMEGTA
0.5 mMTCEP
0.015 % (v/v)Tween20

Details: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.015% Tween20)
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
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: Data were collected using a 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
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: 3916837
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio in cryosparc
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 23577
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 model
PDB IDChain

9qfj

source_name: PDB, initial_model_type: experimental model

5083

source_name: AlphaFold, initial_model_type: in silico model
DetailsPhenix real space refinement
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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