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- PDB-38jl: Cofilactin filament with one AIP1 bound to middle of the filament -

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Basic information

Entry
Database: PDB / ID: 38jl
TitleCofilactin filament with one AIP1 bound to middle of the filament
Components
  • Actin, alpha skeletal muscle
  • Actin-interacting protein 1
  • Cofilin (UNC-60B)
KeywordsSTRUCTURAL PROTEIN / actin / cofilin / AIP1
Function / homology
Function and homology information


muscle thin filament assembly / positive regulation of actin filament depolymerization / negative regulation of actin filament polymerization / regulation of locomotion / actin filament depolymerization / locomotion / sarcomere organization / cytoskeletal motor activator activity / cortical actin cytoskeleton / myosin heavy chain binding ...muscle thin filament assembly / positive regulation of actin filament depolymerization / negative regulation of actin filament polymerization / regulation of locomotion / actin filament depolymerization / locomotion / sarcomere organization / cytoskeletal motor activator activity / cortical actin cytoskeleton / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / sarcoplasm / myofibril / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin filament bundle assembly / actin monomer binding / skeletal muscle fiber development / actin filament polymerization / stress fiber / titin binding / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / lamellipodium / actin binding / cell body / protein domain specific binding / hydrolase activity / positive regulation of gene expression / calcium ion binding / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
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 / WD domain, G-beta repeat ...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 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle / Actin-interacting protein 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsStukey, G.J. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM161161 United States
CitationJournal: To Be Published
Title: AIP1 Promotes Severing of Cofilin-Decorated Actin Filaments by Creating a Stress-Sensitive Rigid-Compliant Boundary
Authors: Stukey, G.J. / Geng, S. / Palmer, N.J. / Saks, A. / Vavylonis, D. / Ono, S. / Dominguez, R.
History
DepositionAug 29, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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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
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
X: Actin-interacting protein 1
a: Cofilin (UNC-60B)
b: Cofilin (UNC-60B)
c: Cofilin (UNC-60B)
d: Cofilin (UNC-60B)
e: Cofilin (UNC-60B)
f: Cofilin (UNC-60B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)508,20331
Polymers504,59115
Non-polymers3,61216
Water72140
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 , 3 types, 15 molecules ABCDEFGHXabcdef

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


Mass: 42096.953 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Actin-interacting protein 1 / AIP1 / Uncoordinated protein 78


Mass: 65392.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-78, C04F6.4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q11176
#3: Protein
Cofilin (UNC-60B)


Mass: 17070.465 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 3 types, 56 molecules

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


Mass: 427.201 Da / Num. of mol.: 8 / 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.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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

ComponentName: Cofilactin filament with one AIP1 bound to middle of the filament
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 51.71 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
7Coot1.1.20model fitting
12cryoSPARC4.73D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111082 / Symmetry type: POINT
RefinementHighest resolution: 2.29 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00436681
ELECTRON MICROSCOPYf_angle_d0.57849932
ELECTRON MICROSCOPYf_dihedral_angle_d6.0125204
ELECTRON MICROSCOPYf_chiral_restr0.0485613
ELECTRON MICROSCOPYf_plane_restr0.0046412

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