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- EMDB-76299: Gelsolin domain G2G3 transitionally bound to F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-76299
TitleGelsolin domain G2G3 transitionally bound to F-actin
Map data
Sample
  • Complex: F-actin bound to gelsolin domains G2 and G3
    • Complex: F-actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: gelsolin
      • Protein or peptide: Gelsolin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
Keywordsgelsolin / actin / STRUCTURAL PROTEIN
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
Gelsolin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsSaks AJ / Dominguez R
Funding support United States, 3 items
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 AJ / Boczkowska M / Barrie KR / Robinson RC / Dominguez R
History
DepositionMar 26, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76299.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.048
Minimum - Maximum-0.11451884 - 0.28812784
Average (Standard dev.)0.00012658004 (±0.0082428185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_76299_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76299_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : F-actin bound to gelsolin domains G2 and G3

EntireName: F-actin bound to gelsolin domains G2 and G3
Components
  • Complex: F-actin bound to gelsolin domains G2 and G3
    • Complex: F-actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: gelsolin
      • Protein or peptide: Gelsolin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION

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Supramolecule #1: F-actin bound to gelsolin domains G2 and G3

SupramoleculeName: F-actin bound to gelsolin domains G2 and G3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 1.5 kDa/nm

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Supramolecule #2: F-actin

SupramoleculeName: F-actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Tissue: Skeletal muscle

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Supramolecule #3: gelsolin

SupramoleculeName: gelsolin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.875633 KDa
SequenceString: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG ...String:
DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Gelsolin

MacromoleculeName: Gelsolin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.451873 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGFKHVVPNE VVVQRLFQVK GRRVVRATEV PVSWESFNNG DCFILDLGNN IHQWCGSNSN RYERLKATQV SKGIRDNERS GRARVHVSE EGTEPEAMLQ VLGPKPALPA GTEDTAKEDA ANRKLAKLYK VSNGAGTMSV SLVADENPFA QGALKSEDCF I LDHGKDGK ...String:
SGFKHVVPNE VVVQRLFQVK GRRVVRATEV PVSWESFNNG DCFILDLGNN IHQWCGSNSN RYERLKATQV SKGIRDNERS GRARVHVSE EGTEPEAMLQ VLGPKPALPA GTEDTAKEDA ANRKLAKLYK VSNGAGTMSV SLVADENPFA QGALKSEDCF I LDHGKDGK IFVWKGKQAN TEERKAALKT ASDFITKMDY PKQTQVSVLP EGGETPLFKQ FFKNWRDPDQ TDGLGLSYLS WS HPQFEK

UniProtKB: Gelsolin

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.42 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
50.0 mMNaClSodium chloride
2.0 mMCaCl2calcium chloride
2.0 mMMgCl2magnesium chloride
0.2 mMATPadenosine triphosphate
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 183304
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8f8p

source_name: PDB, initial_model_type: experimental model

8viz

source_name: PDB, initial_model_type: experimental model
Output model

PDB-12bx:
Gelsolin domain G2G3 transitionally bound to F-actin

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