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- EMDB-43263: Local refinement of G1-G3 and F-actin barbed end subunits B-0 and B-2 -

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Basic information

Entry
Database: EMDB / ID: EMD-43263
TitleLocal refinement of G1-G3 and F-actin barbed end subunits B-0 and B-2
Map dataUnsharpened
Sample
  • Complex: Structure of full-length cytoplasmic gelsolin bound to the barbed end of F-actin
    • Protein or peptide: cytoplasmic gelsolin (His/Strep)
    • Protein or peptide: skeletal actin
Keywordscytoskeleton / actin / cell motility / PROTEIN BINDING
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsBarrie KR / Rebowski G / Dominguez R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM073791 United States
CitationJournal: 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 4, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43263.png

Downloads & links

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Map

FileDownload / File: emd_43263.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 416 pix.
= 449.28 Å		1.08 Å/pix.
x 416 pix.
= 449.28 Å		1.08 Å/pix.
x 416 pix.
= 449.28 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: 0.1
Minimum - Maximum-0.14344533 - 0.4825275
Average (Standard dev.)-0.00007847376 (±0.008934524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 449.28003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43263_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43263_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43263_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 : Structure of full-length cytoplasmic gelsolin bound to the barbed...

EntireName: Structure of full-length cytoplasmic gelsolin bound to the barbed end of F-actin
Components
  • Complex: Structure of full-length cytoplasmic gelsolin bound to the barbed end of F-actin
    • Protein or peptide: cytoplasmic gelsolin (His/Strep)
    • Protein or peptide: skeletal actin

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Supramolecule #1: Structure of full-length cytoplasmic gelsolin bound to the barbed...

SupramoleculeName: Structure of full-length cytoplasmic gelsolin bound to the barbed end of F-actin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Macromolecule #1: cytoplasmic gelsolin (His/Strep)

MacromoleculeName: cytoplasmic gelsolin (His/Strep) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHMVVE HPEFLKAGKE PGLQIWRVEK FDLVPVPTNL YGDFFTGDAY VILKTVQLRN GNLQYDLHYW LGNECSQDES GAAAIFTVQL DDYLNGRAVQ HREVQGFESA TFLGYFKSGL KYKKGGVASG FKHVVPNEVV VQRLFQVKGR RVVRATEVPV SWESFNNGDC ...String:
HHHHHHMVVE HPEFLKAGKE PGLQIWRVEK FDLVPVPTNL YGDFFTGDAY VILKTVQLRN GNLQYDLHYW LGNECSQDES GAAAIFTVQL DDYLNGRAVQ HREVQGFESA TFLGYFKSGL KYKKGGVASG FKHVVPNEVV VQRLFQVKGR RVVRATEVPV SWESFNNGDC FILDLGNNIH QWCGSNSNRY ERLKATQVSK GIRDNERSGR ARVHVSEEGT EPEAMLQVLG PKPALPAGTE DTAKEDAANR KLAKLYKVSN GAGTMSVSLV ADENPFAQGA LKSEDCFILD HGKDGKIFVW KGKQANTEER KAALKTASDF ITKMDYPKQT QVSVLPEGGE TPLFKQFFKN WRDPDQTDGL GLSYLSSHIA NVERVPFDAA TLHTSTAMAA QHGMDDDGTG QKQIWRIEGS NKVPVDPATY GQFYGGDSYI ILYNYRHGGR QGQIIYNWQG AQSTQDEVAA SAILTAQLDE ELGGTPVQSR VVQGKEPAHL MSLFGGKPMI IYKGGTSREG GQTAPASTRL FQVRANSAGA TRAVEVLPKA GALNSNDAFV LKTPSAAYLW VGTGASEAEK TGAQELLRVL RAQPVQVAEG SEPDGFWEAL GGKAAYRTSP RLKDKKMDAH PPRLFACSNK IGRFVIEEVP GELMQEDLAT DDVMLLDTWD QVFVWVGKDS QEEEKTEALT SAKRYIETDP ANRDRRTPIT VVKQGFEPPS FVGWFLGWDD DYWSVDPLDR AMAELAAWSH PQFEK

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Macromolecule #2: skeletal actin

MacromoleculeName: skeletal actin / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
SequenceString: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIITNWD DMEKIWHHTF YNELRVAPEE HPTLLTEAPL NPKANREKMT QIMFETFNVP AMYVAIQAVL SLYASGRTTG IVLDSGDGVT HNVPIYEGYA ...String:
DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIITNWD DMEKIWHHTF YNELRVAPEE HPTLLTEAPL NPKANREKMT QIMFETFNVP AMYVAIQAVL SLYASGRTTG IVLDSGDGVT HNVPIYEGYA LPHAIMRLDL AGRDLTDYLM KILTERGYSF VTTAEREIVR DIKEKLCYVA LDFENEMATA ASSSSLEKSY ELPDGQVITI GNERFRCPET LFQPSFIGME SAGIHETTYN SIMKCDIDIR KDLYANNVMS GGTTMYPGIA DRMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWITKQ EYDEAGPSIV HRKCF

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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94956
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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