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- PDB-8viz: Structure of full-length gelsolin bound to the barbed end of F-actin -

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Basic information

Entry
Database: PDB / ID: 8viz
TitleStructure of full-length gelsolin bound to the barbed end of F-actin
Components
  • Actin, alpha skeletal muscle
  • Gelsolin
KeywordsPROTEIN BINDING / cytoskeleton / actin / cell motility
Function / homology
Function and homology information


striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap ...striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / regulation of podosome assembly / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / barbed-end actin filament capping / actin filament depolymerization / actin filament capping / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / Sensory processing of sound by outer hair cells of the cochlea / podosome / relaxation of cardiac muscle / cytoskeletal motor activator activity / phagocytosis, engulfment / cortical actin cytoskeleton / myosin heavy chain binding / hepatocyte apoptotic process / tropomyosin binding / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / sarcoplasm / skeletal muscle thin filament assembly / actin monomer binding / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / stress fiber / skeletal muscle fiber development / phagocytic vesicle / titin binding / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / central nervous system development / actin filament organization / filopodium / actin filament / protein destabilization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to type II interferon / calcium-dependent protein binding / actin filament binding / lamellipodium / actin cytoskeleton / actin binding / cell body / secretory granule lumen / blood microparticle / amyloid fibril formation / ficolin-1-rich granule lumen / hydrolase activity / protein domain specific binding / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. ...Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 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 / ADENOSINE-5'-TRIPHOSPHATE / Gelsolin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsBarrie, K.R. / Rebowski, G. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM073791 United States
Citation
Journal: Nat Struct Mol Biol / Year: 2025
Title: Mechanism of actin filament severing and capping by gelsolin.
Authors: Kyle R Barrie / Grzegorz Rebowski / Roberto Dominguez /
Abstract: Gelsolin is the prototypical member of a family of Ca-activated F-actin severing and capping proteins. Here we report structures of Ca-bound human gelsolin at the barbed end of F-actin. One structure ...Gelsolin is the prototypical member of a family of Ca-activated F-actin severing and capping proteins. Here we report structures of Ca-bound human gelsolin at the barbed end of F-actin. One structure reveals gelsolin's six domains (G1G6) and interdomain linkers wrapping around F-actin, while another shows domains G1G3-a fragment observed during apoptosis-binding on both sides of F-actin. Conformational changes that trigger severing occur on one side of F-actin with G1G6 and on both sides with G1G3. Gelsolin remains bound after severing, blocking subunit exchange.
#1: Journal: bioRxiv / Year: 2024
Title: Mechanism of Actin Filament Severing and Capping by Gelsolin.
Authors: Kyle R Barrie / Grzegorz Rebowski / Roberto Dominguez
Abstract: Gelsolin is the prototypical member of a family of Ca -dependent F-actin severing and capping proteins. A structure of Ca -bound full-length gelsolin at the barbed end shows domains G1G6 and the ...Gelsolin is the prototypical member of a family of Ca -dependent F-actin severing and capping proteins. A structure of Ca -bound full-length gelsolin at the barbed end shows domains G1G6 and the inter-domain linkers wrapping around F-actin. Another structure shows domains G1G3, a fragment produced during apoptosis, on both sides of F-actin. Conformational changes that trigger severing occur on one side of F-actin with G1G6 and on both sides with G1G3. Gelsolin remains bound after severing, blocking subunit exchange.
History
DepositionJan 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.2Mar 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,19627
Polymers333,9917
Non-polymers3,20420
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 41875.633 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Gelsolin / AGEL / Actin-depolymerizing factor / ADF / Brevin


Mass: 82737.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#3: 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
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSource
1Structure of full-length cytoplasmic gelsolin bound to the barbed end of F-actinCOMPLEX#1-#20MULTIPLE SOURCES
2skeletal actinCOMPLEX1NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Oryctolagus cuniculus (rabbit)9986
32Oryctolagus cuniculus (rabbit)9986
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94956 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00623782
ELECTRON MICROSCOPYf_angle_d1.0432269
ELECTRON MICROSCOPYf_dihedral_angle_d7.1123282
ELECTRON MICROSCOPYf_chiral_restr0.0643543
ELECTRON MICROSCOPYf_plane_restr0.0094163

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