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- EMDB-64130: Severed and capped actin fragment by two G1G3 domains of gelsolin -

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Basic information

Entry
Database: EMDB / ID: EMD-64130
TitleSevered and capped actin fragment by two G1G3 domains of gelsolin
Map datafinal_map_after_deepEMhancer
Sample
  • Complex: Severed and capped actin fragment by gelsolin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Gelsolin
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION
KeywordsCytoskeleton / F-actin / Actin / Actin-binding protein / Gelsolin / CYTOSOLIC 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 / 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
Gelsolin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsKim H / Jung HS
Funding support Korea, Republic Of, 1 items
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 HS
History
DepositionApr 11, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64130.png

Downloads & links

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Map

FileDownload / File: emd_64130.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal_map_after_deepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 500 pix.
= 405. Å		0.81 Å/pix.
x 500 pix.
= 405. Å		0.81 Å/pix.
x 500 pix.
= 405. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.006202387 - 2.248616
Average (Standard dev.)0.00090942415 (±0.023388946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 405.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64130_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: final map before deepEMhancer

Fileemd_64130_additional_1.map
Annotationfinal_map_before_deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_64130_half_map_1.map
Annotationhalf_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_64130_half_map_2.map
Annotationhalf_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Severed and capped actin fragment by gelsolin

EntireName: Severed and capped actin fragment by gelsolin
Components
  • Complex: Severed and capped actin fragment by gelsolin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Gelsolin
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION

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Supramolecule #1: Severed and capped actin fragment by gelsolin

SupramoleculeName: Severed and capped actin fragment by gelsolin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Severed and capped actin fragment by two G1G3 domains of gelsolin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 260 kDa/nm

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1
Details: Severed and capped phalloidin stablized actin fragment by gelsolin
Number of copies: 3 / 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: 875.968 Da
SequenceString:
W(EEP)H(DTH)C(HYP)A

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Macromolecule #2: Gelsolin

MacromoleculeName: Gelsolin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.934766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VEHPEFLKAG KEPGLQIWRV EKFDLVPVPT NLYGDFFTGD AYVILKTVQL RNGNLQYDLH YWLGNECSQD ESGAAAIFTV QLDDYLNGR AVQHREVQGF ESATFLGYFK SGLKYKKGGV ASGFKHVVPN EVVVQRLFQV KGRRVVRATE VPVSWESFNN G DCFILDLG ...String:
VEHPEFLKAG KEPGLQIWRV EKFDLVPVPT NLYGDFFTGD AYVILKTVQL RNGNLQYDLH YWLGNECSQD ESGAAAIFTV QLDDYLNGR AVQHREVQGF ESATFLGYFK SGLKYKKGGV ASGFKHVVPN EVVVQRLFQV KGRRVVRATE VPVSWESFNN G DCFILDLG NNIHQWCGSN SNRYERLKAT QVSKGIRDNE RSGRARVHVS EEGTEPEAML QVLGPKPALP AGTEDTAKED AA NRKLAKL YKVSNGAGTM SVSLVADENP FAQGALKSED CFILDHGKDG KIFVWKGKQA NTEERKAALK TASDFITKMD YPK QTQVSV LPEGGETPLF KQFFKNWRDP DQ

UniProtKB: Gelsolin

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Macromolecule #3: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 3 / Number of copies: 4 / 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: 41.240055 KDa
SequenceString: TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP ...String:
TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP HAIMRLDLAG RDLTDYLMKI LTERGYSFVT TAEREIVRDI KEKLCYVALD FENEMATAAS SSSLEKSY E LPDGQVITIG NERFRCPETL FQPSFIGMES AGIHETTYNS IMKCDIDIRK DLYANNVMSG GTTMYPGIAD RMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWITKQ EYDEAGPSIV HRKC

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / 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 #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38927
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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