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- PDB-12by: Gelsolin domain G2G3 fully bound to F-actin -

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Basic information

Entry
Database: PDB / ID: 12by
TitleGelsolin domain G2G3 fully bound to F-actin
Components
  • Actin, alpha skeletal muscle
  • Gelsolin
KeywordsSTRUCTURAL PROTEIN / gelsolin / actin
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 / positive regulation of keratinocyte apoptotic process / renal protein absorption / positive regulation of protein processing in phagocytic vesicle / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of actin nucleation / actin cap ...striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / positive regulation of keratinocyte apoptotic process / renal protein absorption / positive regulation of protein processing in phagocytic vesicle / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of actin nucleation / actin cap / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / barbed-end actin filament capping / cell projection assembly / actin polymerization or depolymerization / actin filament depolymerization / actin filament capping / relaxation of cardiac muscle / Sensory processing of sound by outer hair cells of the cochlea / phagocytosis, engulfment / cardiac muscle cell contraction / cytoskeletal motor activator activity / myosin heavy chain binding / hepatocyte apoptotic process / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / skeletal muscle myofibril / sarcoplasm / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / cilium assembly / actin monomer binding / Caspase-mediated cleavage of cytoskeletal proteins / skeletal muscle fiber development / phagocytic vesicle / response to muscle stretch / stress fiber / titin binding / actin filament polymerization / phosphatidylinositol-4,5-bisphosphate binding / actin filament organization / central nervous system development / filopodium / actin filament / protein destabilization / cellular response to type II interferon / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 / Amyloid fiber formation / protein domain specific binding / focal adhesion / hydrolase activity / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / magnesium ion binding / : / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
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 / Gelsolin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsSaks, A.J. / Dominguez, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM152412-02 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM073791-20 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM132039-07 United States
CitationJournal: To Be Published
Title: Domains G2G3 Prime the Actin Filament for Severing by Gelsolin
Authors: Saks, A.J. / Boczkowska, M. / Barrie, K.R. / Robinson, R.C. / Dominguez, R.
History
DepositionMar 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 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
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,02427
Polymers364,3329
Non-polymers3,69218
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 42109.973 Da / Num. of mol.: 8 / 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
#2: Protein Gelsolin / AGEL / Actin-depolymerizing factor / ADF / Brevin


Mass: 27451.873 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.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
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
1F-actin bound to gelsolin domains G2 and G3COMPLEX#1-#20MULTIPLE SOURCES
2F-actinCOMPLEX#11NATURAL
3gelsolinCOMPLEX#21RECOMBINANT
Molecular weightValue: 1.5 kDa/nm / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDTissue
13Homo sapiens (human)9606
22Oryctolagus cuniculus (rabbit)9986Skeletal muscle
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
250 mMSodium chlorideNaCl1
32 mMcalcium chlorideCaCl21
42 mMmagnesium chlorideMgCl21
50.2 mMadenosine triphosphateATP1
SpecimenConc.: 0.42 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
9PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 698879 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18F8P

8f8p

18F8P1PDBexperimental model
28VIZ

8viz

18VIZ2PDBexperimental model
RefinementHighest resolution: 2.76 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00525802
ELECTRON MICROSCOPYf_angle_d0.65735006
ELECTRON MICROSCOPYf_dihedral_angle_d12.9669607
ELECTRON MICROSCOPYf_chiral_restr0.0483877
ELECTRON MICROSCOPYf_plane_restr0.0064488

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