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- PDB-9y9j: Two CAP-1 Bound to the Pointed End of Cofilin F-actin -

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Basic information

Entry
Database: PDB / ID: 9y9j
TitleTwo CAP-1 Bound to the Pointed End of Cofilin F-actin
Components
  • Actin, alpha skeletal muscle
  • Adenylyl cyclase-associated protein 1
  • Cofilin-2
KeywordsPROTEIN FIBRIL / Cytoskeleton / Actin / Filament / Helical
Function / homology
Function and homology information


ameboidal-type cell migration / actin filament fragmentation / : / positive regulation of actin filament depolymerization / Role of ABL in ROBO-SLIT signaling / modification of postsynaptic actin cytoskeleton / actin filament severing / actin filament depolymerization / I band / cytoskeletal motor activator activity ...ameboidal-type cell migration / actin filament fragmentation / : / positive regulation of actin filament depolymerization / Role of ABL in ROBO-SLIT signaling / modification of postsynaptic actin cytoskeleton / actin filament severing / actin filament depolymerization / I band / cytoskeletal motor activator activity / sarcomere organization / cortical actin cytoskeleton / muscle cell cellular homeostasis / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / establishment or maintenance of cell polarity / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament / adenylate cyclase binding / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle tissue development / activation of adenylate cyclase activity / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / receptor-mediated endocytosis / actin filament organization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / Z disc / nuclear matrix / calcium-dependent protein binding / actin filament binding / azurophil granule lumen / Platelet degranulation / lamellipodium / actin cytoskeleton / presynapse / actin binding / cell body / postsynapse / protein domain specific binding / focal adhesion / hydrolase activity / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / glutamatergic synapse / magnesium ion binding / signal transduction / : / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / : / CAP N-terminal conserved motif / CAP, N-terminal domain / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP ...Adenylate cyclase-associated CAP, N-terminal / CAP, conserved site, N-terminal / CAP, conserved site, C-terminal / Adenylate cyclase-associated CAP, N-terminal domain superfamily / : / CAP N-terminal conserved motif / CAP, N-terminal domain / CAP protein signature 1. / CAP protein signature 2. / Adenylate cyclase-associated CAP / Adenylate cyclase-associated CAP, C-terminal / Adenylate cyclase associated (CAP) C terminal / Adenylate cyclase-associated CAP, C-terminal superfamily / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / 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 / Actin, alpha skeletal muscle / Adenylyl cyclase-associated protein 1 / Cofilin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 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
Revision 1.1May 13, 2026Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
W: Adenylyl cyclase-associated protein 1
X: Adenylyl cyclase-associated protein 1
a: Cofilin-2
b: Cofilin-2
c: Cofilin-2
d: Cofilin-2
e: Cofilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,91622
Polymers407,65912
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

#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
#2: Protein Adenylyl cyclase-associated protein 1 / CAP 1


Mass: 51968.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAP1, CAP / Production host: Escherichia coli (E. coli) / References: UniProt: Q01518
#3: Protein
Cofilin-2 / Cofilin / muscle isoform


Mass: 18765.627 Da / Num. of mol.: 5
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
#4: 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
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
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-#30MULTIPLE SOURCES
2Cyclase Associated Protein-1COMPLEX#21RECOMBINANT
3Actin, alpha skeletal muscleCOMPLEX#11NATURAL
4Cofilin-2COMPLEX#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Oryctolagus cuniculus (rabbit)9986
54Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Escherichia coli (E. coli)562
44Escherichia 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: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55287 / Symmetry type: POINT
RefinementHighest resolution: 3.58 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00524300
ELECTRON MICROSCOPYf_angle_d0.90932891
ELECTRON MICROSCOPYf_dihedral_angle_d6.3923309
ELECTRON MICROSCOPYf_chiral_restr0.0563684
ELECTRON MICROSCOPYf_plane_restr0.0084175

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