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- PDB-9y9m: Capping protein bound to the barbed end of cofilactin -

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Basic information

Entry
Database: PDB / ID: 9y9m
TitleCapping protein bound to the barbed end of cofilactin
Components
  • (F-actin-capping protein subunit ...) x 2
  • Actin, alpha skeletal muscle
  • Cofilin-2
KeywordsPROTEIN FIBRIL / Cytoskeleton / Actin / Filament / Helical
Function / homology
Function and homology information


actin filament fragmentation / F-actin capping protein complex / WASH complex / positive regulation of actin filament depolymerization / actin filament severing / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament depolymerization / RHOD GTPase cycle ...actin filament fragmentation / F-actin capping protein complex / WASH complex / positive regulation of actin filament depolymerization / actin filament severing / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament depolymerization / RHOD GTPase cycle / regulation of cell morphogenesis / RHOF GTPase cycle / COPI-independent Golgi-to-ER retrograde traffic / lamellipodium assembly / I band / Sensory processing of sound by inner hair cells of the cochlea / cytoskeletal motor activator activity / sarcomere organization / muscle cell cellular homeostasis / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / cortical cytoskeleton / skeletal muscle myofibril / brush border / actin filament bundle assembly / Advanced glycosylation endproduct receptor signaling / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / sperm head-tail coupling apparatus / skeletal muscle tissue development / COPI-mediated anterograde transport / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / cytoskeleton organization / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / hippocampal mossy fiber to CA3 synapse / sarcomere / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / Z disc / nuclear matrix / calcium-dependent protein binding / actin filament binding / lamellipodium / actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / actin binding / actin cytoskeleton organization / cell body / protein-containing complex assembly / cytoskeleton / postsynaptic density / cadherin binding / protein domain specific binding / hydrolase activity / calcium ion binding / positive regulation of gene expression / magnesium ion binding / : / extracellular exosome / extracellular region / ATP binding / membrane / identical protein binding / cytoplasm / cytosol
Similarity search - Function
F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta ...F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / 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 / F-actin-capping protein subunit beta / F-actin-capping protein subunit alpha-1 / Actin, alpha skeletal muscle / Cofilin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsPalmer, N.J. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Adv / Year: 2026
Title: Mechanisms of disassembly at the actin filament pointed and barbed ends.
Authors: Nicholas J Palmer / Malgorzata Boczkowska / Grzegorz Rebowski / Roberto Dominguez /
Abstract: Actin cytoskeleton dynamics power processes from cell motility to organelle trafficking, requiring rapid polymerization and depolymerization accelerated in cells by regulatory proteins. While ...Actin cytoskeleton dynamics power processes from cell motility to organelle trafficking, requiring rapid polymerization and depolymerization accelerated in cells by regulatory proteins. While mechanisms of accelerated polymerization are relatively well studied, those of depolymerization remain poorly understood. Here, we present twelve cryo-electron microscopy structures showing how cofilin, cyclase-associated protein (CAP), and capping protein (CP) coordinate their activities to accelerate depolymerization at both filament ends. Alone, CAP produces a ~4.0 Å lateral displacement of the first pointed-end subunit, whereas cofilin reverts terminal subunits at the pointed and barbed ends to a G-actin-like conformation and undertwists the filament short-pitch helix. When functioning together, these cofilin- and CAP-induced conformational changes are amplified to accelerate pointed-end disassembly. At the barbed end, the cofilin-induced changes trigger stepwise CP dissociation and favor depolymerization. These findings support end-specific mechanisms of filament disassembly through accelerated subunit dissociation, slowed subunit addition, and barbed-end uncapping.
History
DepositionSep 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
Y: F-actin-capping protein subunit alpha-1
Z: F-actin-capping protein subunit beta
a: Cofilin-2
b: Cofilin-2
c: Cofilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,84720
Polymers329,58910
Non-polymers2,25810
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 8 molecules ABCDEabc

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41978.773 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#4: Protein Cofilin-2 / Cofilin / muscle isoform


Mass: 18765.627 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y281

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F-actin-capping protein subunit ... , 2 types, 2 molecules YZ

#2: Protein F-actin-capping protein subunit alpha-1 / CapZ alpha-1


Mass: 32728.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPZA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52907
#3: Protein F-actin-capping protein subunit beta / CapZ beta


Mass: 30669.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPZB / Production host: Escherichia coli (E. coli) / References: UniProt: P47756

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Non-polymers , 2 types, 10 molecules

#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of the Cyclase Associated Protein-1 bound to F-actinCOMPLEX#1-#40MULTIPLE SOURCES
2Actin, alpha skeletal muscleCOMPLEX#11NATURAL
3Cofilin-2COMPLEX#41RECOMBINANT
4Capping ProteinCOMPLEX#2-#31RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
24
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
43Oryctolagus cuniculus (rabbit)9986
54Homo sapiens (human)9606
64Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
44Escherichia coli (E. coli)562
54Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 89000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
5cryoSPARC4.7CTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARC4.7final Euler assignment
13cryoSPARC4.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79486 / Symmetry type: POINT
RefinementHighest resolution: 3.06 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00523114
ELECTRON MICROSCOPYf_angle_d1.08631301
ELECTRON MICROSCOPYf_dihedral_angle_d6.8423157
ELECTRON MICROSCOPYf_chiral_restr0.063485
ELECTRON MICROSCOPYf_plane_restr0.0094004

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