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- PDB-9ug2: Severed and capped actin fragment by two G1G3 domains of gelsolin -

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Basic information

Entry
Database: PDB / ID: 9ug2
TitleSevered and capped actin fragment by two G1G3 domains of gelsolin
Components
  • (Actin, alpha skeletal ...) x 2
  • Gelsolin
KeywordsCYTOSOLIC PROTEIN / Cytoskeleton / F-actin / Actin / Actin-binding protein / Gelsolin
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 / phagocytic vesicle / skeletal muscle fiber development / 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 / cellular response to type II interferon / protein destabilization / 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 / PHOSPHATE ION / Gelsolin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsKim, H. / Jung, H.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Structural insights into the cooperative actin-severing activity of Gelsolin
Authors: Kim, H. / Jung, H.S.
History
DepositionApr 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 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
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Actin, alpha skeletal muscle
A: Gelsolin
B: Gelsolin
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,79928
Polymers245,4589
Non-polymers2,34119
Water00
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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Actin, alpha skeletal ... , 2 types, 7 molecules GHICDEF

#1: Protein/peptide Actin, alpha skeletal muscle


Mass: 875.968 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: Severed and capped phalloidin stablized actin fragment by gelsolin
Source: (natural) Oryctolagus cuniculus (rabbit)
References: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#3: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41240.055 Da / Num. of mol.: 4 / 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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Protein , 1 types, 2 molecules AB

#2: Protein Gelsolin / AGEL / Actin-depolymerizing factor / ADF / Brevin


Mass: 38934.766 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 19 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / 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.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / 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: Severed and capped actin fragment by gelsolin / Type: COMPLEX
Details: Severed and capped actin fragment by two G1G3 domains of gelsolin
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 260 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38927 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 85.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003517372
ELECTRON MICROSCOPYf_angle_d0.63323553
ELECTRON MICROSCOPYf_chiral_restr0.04582583
ELECTRON MICROSCOPYf_plane_restr0.00373026
ELECTRON MICROSCOPYf_dihedral_angle_d7.24912445

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