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- EMDB-43316: Structure of gelsolin domains G1G3 bound to the barbed end of F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-43316
TitleStructure of gelsolin domains G1G3 bound to the barbed end of F-actin
Map data
Sample
  • Complex: Structure of gelsolin domains G1-G3 bound to both strands on the barbed end of F-actin
    • Complex: skeletal actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Gelsolin
      • Protein or peptide: Gelsolin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordscytoskeleton / actin / cell motility / PROTEIN BINDING
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 / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / : ...striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / : / actin cap / regulation of podosome assembly / : / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / barbed-end actin filament capping / actin filament depolymerization / actin filament capping / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / podosome / cytoskeletal motor activator activity / phagocytosis, engulfment / cortical actin cytoskeleton / tropomyosin binding / hepatocyte apoptotic process / mesenchyme migration / myosin heavy chain binding / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / sarcoplasm / actin monomer binding / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / stress fiber / skeletal muscle fiber development / titin binding / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / actin filament organization / filopodium / central nervous system development / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / cellular response to type II interferon / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell body / secretory granule lumen / blood microparticle / ficolin-1-rich granule lumen / amyloid fibril formation / hydrolase activity / protein domain specific binding / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
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: 3.63 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 9, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43316.png

Downloads & links

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Map

FileDownload / File: emd_43316.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.26355606 - 0.76367736
Average (Standard dev.)-0.0005208081 (±0.024260258)
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_43316_msk_1.map
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Histogram

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Half map: #2

Fileemd_43316_half_map_1.map
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Histogram

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Half map: #1

Fileemd_43316_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Structure of gelsolin domains G1-G3 bound to both strands on the ...

EntireName: Structure of gelsolin domains G1-G3 bound to both strands on the barbed end of F-actin
Components
  • Complex: Structure of gelsolin domains G1-G3 bound to both strands on the barbed end of F-actin
    • Complex: skeletal actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Gelsolin
      • Protein or peptide: Gelsolin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Structure of gelsolin domains G1-G3 bound to both strands on the ...

SupramoleculeName: Structure of gelsolin domains G1-G3 bound to both strands on the barbed end of F-actin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: skeletal actin

SupramoleculeName: skeletal actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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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: 6 / Enantiomer: LEVO
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.606484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHMVVE HPEFLKAGKE PGLQIWRVEK FDLVPVPTNL YGDFFTGDAY VILKTVQLRN GNLQYDLHYW LGNECSQDES GAAAIFTVQ LDDYLNGRAV QHREVQGFES ATFLGYFKSG LKYKKGGVAS GFKHVVPNEV VVQRLFQVKG RRVVRATEVP V SWESFNNG ...String:
HHHHHHMVVE HPEFLKAGKE PGLQIWRVEK FDLVPVPTNL YGDFFTGDAY VILKTVQLRN GNLQYDLHYW LGNECSQDES GAAAIFTVQ LDDYLNGRAV QHREVQGFES ATFLGYFKSG LKYKKGGVAS GFKHVVPNEV VVQRLFQVKG RRVVRATEVP V SWESFNNG DCFILDLGNN IHQWCGSNSN RYERLKATQV SKGIRDNERS GRARVHVSEE GTEPEAMLQV LGPKPALPAG TE DTAKEDA ANRKLAKLYK VSNGAGTMSV SLVADENPFA QGALKSEDCF ILDHGKDGKI FVWKGKQANT EERKAALKTA SDF ITKMDY PKQTQVSVLP EGGETPLFKQ FFKNWRDPDQ TDGLGLSYLS SHIANVERVP FDAATLHTST AMAAQHGMDD DGTG QKQIW RIEGSNKVPV DPATYGQFYG GDSYIILYNY RHGGRQGQII YNWQGAQSTQ DEVAASAILT AQLDEELGGT PVQSR VVQG KEPAHLMSLF GGKPMIIYKG GTSREGGQTA PASTRLFQVR ANSAGATRAV EVLPKAGALN SNDAFVLKTP SAAYLW VGT GASEAEKTGA QELLRVLRAQ PVQVAEGSEP DGFWEALGGK AAYRTSPRLK DKKMDAHPPR LFACSNKIGR FVIEEVP GE LMQEDLATDD VMLLDTWDQV FVWVGKDSQE EEKTEALTSA KRYIETDPAN RDRRTPITVV KQGFEPPSFV GWFLGWDD D YWSVDPLDRA MAELAAWSHP QFEK

UniProtKB: Gelsolin

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / 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 #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 14 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12808
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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