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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 / Cell-extracellular matrix interactions / RHO GTPases activate IQGAPs / GBP-mediated host defense / Adherens junctions interactions / Regulation of CDH1 Function / Formation of the dystrophin-glycoprotein complex (DGC) / RHO GTPases Activate Formins / Advanced glycosylation endproduct receptor signaling / RHOBTB2 GTPase cycle ...cytoskeletal calyx / Cell-extracellular matrix interactions / RHO GTPases activate IQGAPs / GBP-mediated host defense / Adherens junctions interactions / Regulation of CDH1 Function / Formation of the dystrophin-glycoprotein complex (DGC) / RHO GTPases Activate Formins / Advanced glycosylation endproduct receptor signaling / RHOBTB2 GTPase cycle / Gap junction degradation / Formation of annular gap junctions / activation of protein kinase C activity / EPHB-mediated forward signaling / negative regulation of filopodium assembly / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / regulation of cell morphogenesis / F-actin capping protein complex / WASH complex / sperm head / VEGFA-VEGFR2 Pathway / sperm head-tail coupling apparatus / cellular response to cytochalasin B / cell projection organization / Clathrin-mediated endocytosis / regulation of transepithelial transport / cell junction assembly / morphogenesis of a polarized epithelium / actin polymerization or depolymerization / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / barbed-end actin filament capping / muscle cell development / dense body / regulation of lamellipodium assembly / Tat protein binding / postsynaptic actin cytoskeleton / apical protein localization / lamellipodium assembly / adherens junction assembly / tight junction / apical junction complex / negative regulation of microtubule polymerization / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / transporter regulator activity / cortical cytoskeleton / establishment or maintenance of cell polarity / nitric-oxide synthase binding / brush border / intercalated disc / regulation of synaptic vesicle endocytosis / kinesin binding / cell morphogenesis / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / beta-tubulin binding / axonogenesis / cytoskeleton organization / calyx of Held / cell motility / nitric-oxide synthase regulator activity / hippocampal mossy fiber to CA3 synapse / actin filament / adherens junction / Schaffer collateral - CA1 synapse / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / neuron projection development / Z disc / cytoplasmic ribonucleoprotein granule / cell-cell junction / actin cytoskeleton organization / actin cytoskeleton / lamellipodium / actin binding / dendritic spine / cytoskeleton / regulation of cell cycle / postsynaptic density / ribonucleoprotein complex / axon / focal adhesion / neuronal cell body / synapse / protein kinase binding / glutamatergic synapse / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / 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
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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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Structure visualization

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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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