[English] 日本語
Yorodumi
- PDB-9qfj: Cryo-EM structure of the cofilactin filament core at 2.3 Angstrom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qfj
TitleCryo-EM structure of the cofilactin filament core at 2.3 Angstrom resolution.
Components
  • Actin, cytoplasmic 1, N-terminally processed
  • Cofilin-1
KeywordsSTRUCTURAL PROTEIN / actin / cofilin / filament / cytoskeleton
Function / homology
Function and homology information


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 / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / actin filament fragmentation / positive regulation of actin filament depolymerization ...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 / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / actin filament fragmentation / positive regulation of actin filament depolymerization / negative regulation of actin filament bundle assembly / modification of postsynaptic actin cytoskeleton / positive regulation of embryonic development / positive regulation of norepinephrine uptake / negative regulation of actin filament depolymerization / positive regulation of cell motility / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / actin filament severing / host-mediated activation of viral process / regulation of transepithelial transport / Formation of the canonical BAF (cBAF) complex / negative regulation of cell adhesion / positive regulation of synaptic plasticity / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / Formation of the polybromo-BAF (pBAF) complex / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / GBP-mediated host defense / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / protein localization to adherens junction / Formation of the non-canonical BAF (ncBAF) complex / Cell-extracellular matrix interactions / establishment of spindle localization / regulation of G0 to G1 transition / regulation of dendritic spine morphogenesis / dense body / negative regulation of cell motility / Tat protein binding / actin filament depolymerization / Folding of actin by CCT/TriC / RHO GTPases Activate ROCKs / cellular response to interleukin-6 / postsynaptic actin cytoskeleton / Regulation of CDH1 Function / apical protein localization / Adherens junctions interactions / microtubule nucleation / Prefoldin mediated transfer of substrate to CCT/TriC / RHOF GTPase cycle / adherens junction assembly / regulation of double-strand break repair / negative regulation of dendritic spine maintenance / Sensory processing of sound by outer hair cells of the cochlea / tight junction / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / cellular response to insulin-like growth factor stimulus / positive regulation of T cell differentiation / maintenance of blood-brain barrier / Interaction between L1 and Ankyrins / cortical actin cytoskeleton / positive regulation of dendritic spine development / apical junction complex / phosphatidylinositol bisphosphate binding / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / positive regulation of proteolysis / transporter regulator activity / Recycling pathway of L1 / cortical cytoskeleton / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / lamellipodium membrane / negative regulation of cell differentiation / establishment or maintenance of cell polarity / mitotic cytokinesis / nitric-oxide synthase binding / cellular response to interleukin-1 / Sema3A PAK dependent Axon repulsion / brush border / EPH-ephrin mediated repulsion of cells / Rho protein signal transduction / positive regulation of focal adhesion assembly / positive regulation of myoblast differentiation / regulation of synaptic vesicle endocytosis / RHO GTPases Activate WASPs and WAVEs / kinesin binding / positive regulation of lamellipodium assembly / postsynaptic density, intracellular component / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of G1/S transition of mitotic cell cycle / axonogenesis / cytoskeleton organization
Similarity search - Function
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 ...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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cofilin-1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.31 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 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: Cofilin-1
F: Cofilin-1
H: Cofilin-1
I: Cofilin-1
J: Cofilin-1
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,08220
Polymers300,82510
Non-polymers2,25810
Water15,439857
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_1ens_2chain "F"
d_2ens_2chain "G"
d_3ens_2chain "H"
d_4ens_2chain "I"
d_5ens_2chain "J"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAPHEPHEAF6 - 3755 - 374
d_12ens_1ADPADPADPADPAK401
d_21ens_1ALAALAPHEPHEBG6 - 3755 - 374
d_22ens_1ADPADPADPADPBM401
d_31ens_1ALAALAPHEPHECH6 - 3755 - 374
d_32ens_1ADPADPADPADPCO401
d_41ens_1ALAALAPHEPHEDI6 - 3755 - 374
d_42ens_1ADPADPADPADPDQ401
d_51ens_1ALAALAPHEPHEEJ6 - 3755 - 374
d_52ens_1ADPADPADPADPES401
d_11ens_2ALAALALEULEUFB2 - 1662 - 166
d_21ens_2ALAALALEULEUGA2 - 1662 - 166
d_31ens_2ALAALALEULEUHC2 - 1662 - 166
d_41ens_2ALAALALEULEUID2 - 1662 - 166
d_51ens_2ALAALALEULEUJE2 - 1662 - 166

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.954395776068, 0.298541868328, -0.00120643188221), (-0.298541801059, -0.954396529531, -0.00023966662181), (-0.00122296492255, 0.000131433535451, 0.999999243541)252.389107257, 343.152430304, 27.4681417363
2given(0.821995207042, -0.569494339908, 0.000276427431356), (0.569494359121, 0.821995240136, 1.10457272053E-5), (-0.000233512511941, 0.000148344328043, 0.999999961733)113.802736915, -59.6437136038, 54.6108524553
3given(-0.614175469714, 0.789169063235, -0.000825853924864), (-0.789169409073, -0.61417555562, 0.000175104926258), (-0.000369031902541, 0.0007592838042, 0.999999643652)125.766354155, 366.027217839, 81.8600803291
4given(0.350576631797, -0.936534045956, 7.74739431263E-5), (0.936533893687, 0.350576524732, -0.000605212391734), (0.000539641464155, 0.000284730295431, 0.999999813858)241.521847658, -43.7036977086, 109.07829803
5given(-0.954520692622, 0.298144267063, -0.000493329367053), (-0.298143948348, -0.954520712588, -0.000628732683915), (-0.000658346144204, -0.000453055191596, 0.999999680661)252.390480917, 343.177336274, 27.4623620664
6given(0.821684239292, -0.569942874947, -0.000360827212125), (0.56994297967, 0.821683945363, 0.000702749556498), (-0.000104041175346, -0.000783089171168, 0.999999687973)113.956973061, -59.7812223452, 54.760117583
7given(-0.614222193587, 0.789132975531, -0.000493796240549), (-0.789131525541, -0.614222086325, -0.00163219726478), (-0.0015913212413, -0.000612861603727, 0.999998546048)125.756626425, 366.269245109, 82.2414803114
8given(0.351140869023, -0.93631008228, -0.00484973432206), (0.936322493955, 0.351139016892, 0.0012562367472), (0.000526703809906, -0.00498203139856, 0.999987450894)241.913549971, -43.9944211649, 109.776210684

-
Components

#1: 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
#2: 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
#3: 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1Cofilactin filament coreCOMPLEXCofilin-1 bound to the actin filament#1-#20MULTIPLE SOURCES
2Actin filamentCOMPLEX#21RECOMBINANT
3Cofilin-1COMPLEX#11RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Trichoplusia ni (cabbage looper)7111
32Trichoplusia ni (cabbage looper)7111
43Escherichia coli (E. coli)562
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% Tween)
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES1
2100 mMpotassium chlorideKCl1
32 mMmagnesium chlorideMgCl21
41 mMEGTA1
50.5 mMTCEP1
60.015 % (v/v)Tween1
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

-
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 magnification: 105000 X / 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: 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) equipped with an in-column Cs corrector

-
Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.4particle selectionFilament Tracer
2EPUimage acquisition
4cryoSPARC4.4CTF correctionPatch CTF
7UCSF ChimeraX1.8model fitting
8Coot0.9.8.1model fitting
10cryoSPARC4.4initial Euler assignment
11cryoSPARC4.4final Euler assignment
12cryoSPARC4.4classification
13cryoSPARC4.43D reconstructionLocal Refinement
14PHENIX1.21rc1_5015model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8428096
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4767360 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: The final model refinement was performed using Phenix real space refinement.
Atomic model buildingPDB-ID: 6VAO

6vao


Accession code: 6VAO / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 45.56 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003321015
ELECTRON MICROSCOPYf_angle_d0.51228425
ELECTRON MICROSCOPYf_chiral_restr0.04373190
ELECTRON MICROSCOPYf_plane_restr0.00323605
ELECTRON MICROSCOPYf_dihedral_angle_d11.14277865
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FAELECTRON MICROSCOPYNCS constraints4.19399737636E-11
ens_1d_3FAELECTRON MICROSCOPYNCS constraints3.62372616534E-13
ens_1d_4FAELECTRON MICROSCOPYNCS constraints8.54927136354E-12
ens_1d_5FAELECTRON MICROSCOPYNCS constraints2.88453540874E-13
ens_2d_2BFELECTRON MICROSCOPYNCS constraints1.04917595535E-11
ens_2d_3BFELECTRON MICROSCOPYNCS constraints2.9188028929E-11
ens_2d_4BFELECTRON MICROSCOPYNCS constraints3.95891773946E-13
ens_2d_5BFELECTRON MICROSCOPYNCS constraints2.38445234816E-12

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more