[English] 日本語
Yorodumi
- PDB-9qew: Cryo-EM structure of the undecorated actin filament in the ADP-Pi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qew
TitleCryo-EM structure of the undecorated actin filament in the ADP-Pi state.
ComponentsActin, cytoplasmic 1, N-terminally processed
KeywordsSTRUCTURAL PROTEIN / actin / filament / cytoskeleton
Function / homology
Function and homology information


positive regulation of norepinephrine uptake / bBAF complex / cellular response to cytochalasin B / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / morphogenesis of a polarized epithelium ...positive regulation of norepinephrine uptake / bBAF complex / cellular response to cytochalasin B / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / GBAF complex / Folding of actin by CCT/TriC / regulation of G0 to G1 transition / protein localization to adherens junction / Cell-extracellular matrix interactions / dense body / Tat protein binding / postsynaptic actin cytoskeleton / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / regulation of double-strand break repair / regulation of nucleotide-excision repair / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / 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 T cell differentiation / apical junction complex / positive regulation of double-strand break repair / maintenance of blood-brain barrier / regulation of norepinephrine uptake / nitric-oxide synthase binding / transporter regulator activity / cortical cytoskeleton / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / positive regulation of stem cell population maintenance / Recycling pathway of L1 / Regulation of MITF-M-dependent genes involved in pigmentation / brush border / regulation of G1/S transition of mitotic cell cycle / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / kinesin binding / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / EPHB-mediated forward signaling / cytoskeleton organization / substantia nigra development / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / actin filament / adherens junction / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / Regulation of actin dynamics for phagocytic cup formation / B-WICH complex positively regulates rRNA expression / kinetochore / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / VEGFA-VEGFR2 Pathway / platelet aggregation / Schaffer collateral - CA1 synapse / tau protein binding / nuclear matrix / cytoplasmic ribonucleoprotein granule / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / UCH proteinases / nucleosome / presynapse / lamellipodium / actin cytoskeleton / Clathrin-mediated endocytosis / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production
Similarity search - Function
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 / PHOSPHATE ION / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.18 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Actin, cytoplasmic 1, N-terminally processed
A: Actin, cytoplasmic 1, N-terminally processed
B: 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)210,89420
Polymers208,1625
Non-polymers2,73215
Water12,430690
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Many structures.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "D"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "A"
d_5ens_1chain "E"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAPHEPHEDD6 - 3755 - 374
d_12ADPADPADPADPDO401
d_13MGMGMGMGDP402
d_14PO4PO4PO4PO4DQ403
d_21ALAALAPHEPHEBC6 - 3755 - 374
d_22ADPADPADPADPBL401
d_23MGMGMGMGBM402
d_24PO4PO4PO4PO4BN403
d_31ALAALAPHEPHECA6 - 3755 - 374
d_32ADPADPADPADPCF401
d_33MGMGMGMGCG402
d_34PO4PO4PO4PO4CH403
d_41ALAALAPHEPHEAB6 - 3755 - 374
d_42ADPADPADPADPAI401
d_43MGMGMGMGAJ402
d_44PO4PO4PO4PO4AK403
d_51ALAALAPHEPHEEE6 - 3755 - 374
d_52ADPADPADPADPER401
d_53MGMGMGMGES402
d_54PO4PO4PO4PO4ET403

NCS oper:
IDCodeMatrixVector
1given(0.892190691496, -0.451658397695, 0.000679558400688), (0.451657951809, 0.892190888465, 0.00071631532867), (-0.000929825646865, -0.000332161913026, 0.999999512546)72.9822547231, -44.9028177902, 55.0768288496
2given(-0.972229972781, 0.233992028058, -0.00407563888056), (-0.234007237182, -0.972227558134, 0.00376671625675), (-0.00308106686065, 0.00461584343797, 0.99998460039)227.260693224, 287.74210031, 27.2991452083
3given(-0.763106788746, 0.646271994228, -0.000733789482674), (-0.646271753389, -0.763103901079, 0.00229279968691), (0.000921814609226, 0.0022238784219, 0.999997102307)145.789563806, 314.431494539, 81.963014052
4given(-0.972681005422, -0.232145532745, 0.000336626117332), (0.232145314505, -0.972675151852, 0.00340615959519), (-0.000463296874049, 0.00339125291556, 0.999994142363)287.73976559, 226.743507858, -27.8145637122

-
Components

#1: 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
Details: Filament / Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Cell line (production host): BTI-Tnao38 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60709
#2: 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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / 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

ComponentName: Beta-actin filament. / Type: COMPLEX
Details: The filament is double stranded and consists of beta-actin subunits.
Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper) / Cell: BTI-Tnao38
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, 0.01% Tween20).
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES1
2100 mMpotassium chlorideKCl1
32 mMmagnesium chlorideMgCl21
41 mMEGTA1
50.5 mMTCEP1
60.01 % (v/v)Tween201
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: 68.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 21841
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV
Spherical aberration corrector: The used Titan Krios G2 microscope contains an in-column Cs corrector.

-
Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4particle selectionFilament tracer
2EPUimage acquisition
4cryoSPARC4.4CTF correctionPatch CTF
7Coot0.9.8.1model fitting
8UCSF ChimeraX1.8model fitting
10cryoSPARC4.4initial Euler assignment
11cryoSPARC4.4final Euler assignment
12cryoSPARC4.4classification
13cryoSPARC4.43D reconstructionLocal Refinement
14PHENIX1.21rc1_5015model refinement
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9946495
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4674353 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: Phenix real space refinement.
Atomic model buildingPDB-ID: 8OI8

8oi8


Accession code: 8OI8 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 35.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004214905
ELECTRON MICROSCOPYf_angle_d0.559420225
ELECTRON MICROSCOPYf_chiral_restr0.04612240
ELECTRON MICROSCOPYf_plane_restr0.00392580
ELECTRON MICROSCOPYf_dihedral_angle_d11.99495530
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DDELECTRON MICROSCOPYNCS constraints7.51410085708E-12
ens_1d_3DDELECTRON MICROSCOPYNCS constraints8.77664117408E-12
ens_1d_4DDELECTRON MICROSCOPYNCS constraints3.43497694801E-13
ens_1d_5DDELECTRON MICROSCOPYNCS constraints2.4387893107E-13

+
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