9Y52 | pdb_00009y52

One CAP-1 Bound to the Pointed End of Cofilin F-actin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9Y52

This is version 1.1 of the entry. See complete history

Literature

Mechanisms of disassembly at the actin filament pointed and barbed ends.

Palmer, N.J.Boczkowska, M.Rebowski, G.Dominguez, R.

(2026) Sci Adv 12: eaee5882-eaee5882

  • DOI: https://doi.org/10.1126/sciadv.aee5882
  • Primary Citation Related Structures: 
    9Q7K, 9Q7L, 9Q7M, 9Q7N, 9Q7O, 9XYE, 9Y52, 9Y9J, 9Y9L, 9Y9M, 9Y9P, 9YIM

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Department of Physiology and Biochemistry Biophysics & Chemical Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.

Macromolecule Content 

  • Total Structure Weight: 357.95 kDa 
  • Atom Count: 22,387 
  • Modeled Residue Count: 2,826 
  • Deposited Residue Count: 3,185 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle
A, B, C, D, E
376Oryctolagus cuniculusMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68135
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Adenylyl cyclase-associated protein 1F [auth W]475Homo sapiensMutation(s): 0 
Gene Names: CAP1CAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q01518 (Homo sapiens)
Explore Q01518 
Go to UniProtKB:  Q01518
PHAROS:  Q01518
GTEx:  ENSG00000131236 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01518
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cofilin-2G [auth a],
H [auth b],
I [auth c],
J [auth d],
K [auth e]
166Homo sapiensMutation(s): 0 
Gene Names: CFL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y281 (Homo sapiens)
Explore Q9Y281 
Go to UniProtKB:  Q9Y281
PHAROS:  Q9Y281
GTEx:  ENSG00000165410 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y281
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
L [auth A],
N [auth B],
P [auth C],
R [auth D],
T [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
A, B, C, D, E
L-PEPTIDE LINKINGC7 H11 N3 O2HIS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.7

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-04
    Type: Initial release
  • Version 1.1: 2026-05-13
    Changes: Data collection, Database references