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- PDB-9yim: Capping protein bound to the barbed end of F-actin -

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Basic information

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


F-actin capping protein complex / WASH complex / sperm head-tail coupling apparatus / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / RHOD GTPase cycle / regulation of cell morphogenesis / RHOF GTPase cycle / COPI-independent Golgi-to-ER retrograde traffic ...F-actin capping protein complex / WASH complex / sperm head-tail coupling apparatus / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / RHOD GTPase cycle / regulation of cell morphogenesis / RHOF GTPase cycle / COPI-independent Golgi-to-ER retrograde traffic / Sensory processing of sound by inner hair cells of the cochlea / lamellipodium assembly / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / cortical cytoskeleton / mesenchyme migration / skeletal muscle myofibril / brush border / Advanced glycosylation endproduct receptor signaling / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / 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 / sarcomere / hippocampal mossy fiber to CA3 synapse / actin filament / filopodium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / Factors involved in megakaryocyte development and platelet production / actin binding / cell body / actin cytoskeleton organization / 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 / identical protein binding / membrane / 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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 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: To Be Published
Title: Mechanisms of Actin Filament Depolymerization by Cyclase Associated Protein-1 and Cofilin-2
Authors: Palmer, N.J. / Boczkowska, M. / Rebowski, G. / Dominguez, R.
History
DepositionOct 1, 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: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,67117
Polymers269,4137
Non-polymers2,25810
Water1629
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 , 1 types, 5 molecules ABCDE

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


Mass: 41387.227 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

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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: 32041.746 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: 30435.432 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 , 3 types, 19 molecules

#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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-#30MULTIPLE SOURCES
2Actin, alpha skeletal muscleCOMPLEX#11NATURAL
3Capping ProteinCOMPLEX#2-#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
52Oryctolagus cuniculus (rabbit)9986
63Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
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: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 275590 / Symmetry type: POINT
RefinementHighest resolution: 2.62 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00519435
ELECTRON MICROSCOPYf_angle_d1.03826350
ELECTRON MICROSCOPYf_dihedral_angle_d7.2222677
ELECTRON MICROSCOPYf_chiral_restr0.0632911
ELECTRON MICROSCOPYf_plane_restr0.0093387

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