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- PDB-7pdz: Structure of capping protein bound to the barbed end of a cytopla... -

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Basic information

Entry
Database: PDB / ID: 7pdz
TitleStructure of capping protein bound to the barbed end of a cytoplasmic actin filament
Components
  • Actin, cytoplasmic 1
  • F-actin-capping protein subunit alpha-1
  • Isoform 2 of F-actin-capping protein subunit beta
  • Phalloidin
KeywordsSTRUCTURAL PROTEIN / Cytoskeleton / cell-shape remodelling / barbed end
Function / homology
Function and homology information


cytoskeletal calyx / regulation of protein kinase C signaling / Cell-extracellular matrix interactions / Adherens junctions interactions / Formation of the dystrophin-glycoprotein complex (DGC) / Advanced glycosylation endproduct receptor signaling / B-WICH complex positively regulates rRNA expression / RHOF GTPase cycle / Gap junction degradation / Formation of annular gap junctions ...cytoskeletal calyx / regulation of protein kinase C signaling / Cell-extracellular matrix interactions / Adherens junctions interactions / Formation of the dystrophin-glycoprotein complex (DGC) / Advanced glycosylation endproduct receptor signaling / B-WICH complex positively regulates rRNA expression / RHOF GTPase cycle / Gap junction degradation / Formation of annular gap junctions / RHOD GTPase cycle / MAP2K and MAPK activation / RHOF GTPase cycle / COPI-independent Golgi-to-ER retrograde traffic / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / COPI-mediated anterograde transport / sperm head-tail coupling apparatus / DNA Damage Recognition in GG-NER / F-actin capping protein complex / WASH complex / UCH proteinases / sperm head / VEGFA-VEGFR2 Pathway / Factors involved in megakaryocyte development and platelet production / cellular response to cytochalasin B / regulation of transepithelial transport / Clathrin-mediated endocytosis / cell junction assembly / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / barbed-end actin filament capping / MHC class II antigen presentation / protein localization to adherens junction / dense body / actin polymerization or depolymerization / Tat protein binding / cell projection organization / muscle cell development / postsynaptic actin cytoskeleton / regulation of cell morphogenesis / adherens junction assembly / apical protein localization / tight junction / lamellipodium assembly / apical junction complex / regulation of norepinephrine uptake / negative regulation of microtubule polymerization / nitric-oxide synthase binding / transporter regulator activity / cortical cytoskeleton / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / brush border / asymmetric synapse / intercalated disc / kinesin binding / regulation of synaptic vesicle endocytosis / beta-tubulin binding / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / cytoskeleton organization / axonogenesis / calyx of Held / hippocampal mossy fiber to CA3 synapse / nitric-oxide synthase regulator activity / actin filament / adherens junction / cell motility / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / Z disc / cytoplasmic ribonucleoprotein granule / neuron projection development / cell-cell junction / nucleosome / lamellipodium / actin cytoskeleton / actin binding / cytoskeleton / regulation of cell cycle / postsynaptic density / ribonucleoprotein complex / axon / focal adhesion / synapse / protein kinase binding / glutamatergic synapse / protein-containing complex / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm
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
Phalloidin / ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bos taurus (domestic cattle)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsFunk, J. / Merino, F. / Schacks, M. / Rottner, K. / Raunser, S. / Bieling, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2021
Title: A barbed end interference mechanism reveals how capping protein promotes nucleation in branched actin networks.
Authors: Johanna Funk / Felipe Merino / Matthias Schaks / Klemens Rottner / Stefan Raunser / Peter Bieling /
Abstract: Heterodimeric capping protein (CP/CapZ) is an essential factor for the assembly of branched actin networks, which push against cellular membranes to drive a large variety of cellular processes. Aside ...Heterodimeric capping protein (CP/CapZ) is an essential factor for the assembly of branched actin networks, which push against cellular membranes to drive a large variety of cellular processes. Aside from terminating filament growth, CP potentiates the nucleation of actin filaments by the Arp2/3 complex in branched actin networks through an unclear mechanism. Here, we combine structural biology with in vitro reconstitution to demonstrate that CP not only terminates filament elongation, but indirectly stimulates the activity of Arp2/3 activating nucleation promoting factors (NPFs) by preventing their association to filament barbed ends. Key to this function is one of CP's C-terminal "tentacle" extensions, which sterically masks the main interaction site of the terminal actin protomer. Deletion of the β tentacle only modestly impairs capping. However, in the context of a growing branched actin network, its removal potently inhibits nucleation promoting factors by tethering them to capped filament ends. End tethering of NPFs prevents their loading with actin monomers required for activation of the Arp2/3 complex and thus strongly inhibits branched network assembly both in cells and reconstituted motility assays. Our results mechanistically explain how CP couples two opposed processes-capping and nucleation-in branched actin network assembly.
History
DepositionAug 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
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Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.2Oct 1, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
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Revision 1.1Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
E: Isoform 2 of F-actin-capping protein subunit beta
F: F-actin-capping protein subunit alpha-1
I: Actin, cytoplasmic 1
J: Actin, cytoplasmic 1
K: Actin, cytoplasmic 1
L: Actin, cytoplasmic 1
N: Actin, cytoplasmic 1
O: Actin, cytoplasmic 1
Q: Phalloidin
R: Phalloidin
S: Phalloidin
T: Phalloidin
P: Phalloidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,55829
Polymers318,46913
Non-polymers3,08916
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area37550 Å2
ΔGint-341 kcal/mol
Surface area109870 Å2
MethodPISA

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Components

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Protein , 3 types, 8 molecules EFIJKLNO

#1: Protein Isoform 2 of 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.) Mus musculus (house mouse) / Gene: Capzb, Cappb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P47757
#2: Protein F-actin-capping protein subunit alpha-1 / CapZ alpha-1


Mass: 32980.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Capza1, Cappa1 / Production host: Escherichia coli (E. coli) / References: UniProt: P47753
#3: Protein
Actin, cytoplasmic 1 / Beta-actin


Mass: 41795.680 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P60712

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Protein/peptide , 1 types, 5 molecules QRSTP

#4: Protein/peptide
Phalloidin


Type: Cyclic peptide / Class: Toxin / Mass: 808.899 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Phalloidin

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Non-polymers , 3 types, 16 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Complex between capping protein and the barbed end of cytoplasmic actin filaments
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Buffer solutionpH: 7 / Details: KMEI buffer
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMPotassium chlorideKCl1
210 mMImidazole1
31.5 mMMagnesium chlorideMgCl21
41 mMEGTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Mild discharging with 5 mA current / Grid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 286 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 3 sec. / Electron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4204

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1.13CTF correction
7UCSF Chimeramodel fitting
9SPHIRE1.3initial Euler assignment
10SPHIRE1.3final Euler assignment
11SPHIRE1.3classification
12SPHIRE1.33D reconstruction
13ISOLDEmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 570724
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60206 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 40 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 5ADX

5adx


Accession code: 5ADX / Source name: PDB / Type: experimental model

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