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- EMDB-17555: Cryo-EM structure of cortactin-stabilized Arp2/3-complex nucleate... -

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Basic information

Entry
Database: EMDB / ID: EMD-17555
TitleCryo-EM structure of cortactin-stabilized Arp2/3-complex nucleated actin branches-Local refined map on the daughter filament and cortactin density
Map dataunsharpened
Sample
  • Complex: Cortactin-stabilized Arp2/3-complex nucleated actin branches
KeywordsComplex / CONTRACTILE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiu T / Moores CA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)810207European Union
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Cortactin stabilizes actin branches by bridging activated Arp2/3 to its nucleated actin filament.
Authors: Tianyang Liu / Luyan Cao / Miroslav Mladenov / Antoine Jegou / Michael Way / Carolyn A Moores /
Abstract: Regulation of the assembly and turnover of branched actin filament networks nucleated by the Arp2/3 complex is essential during many cellular processes, including cell migration and membrane ...Regulation of the assembly and turnover of branched actin filament networks nucleated by the Arp2/3 complex is essential during many cellular processes, including cell migration and membrane trafficking. Cortactin is important for actin branch stabilization, but the mechanism by which this occurs is unclear. Given this, we determined the structure of vertebrate cortactin-stabilized Arp2/3 actin branches using cryogenic electron microscopy. We find that cortactin interacts with the new daughter filament nucleated by the Arp2/3 complex at the branch site, rather than the initial mother actin filament. Cortactin preferentially binds activated Arp3. It also stabilizes the F-actin-like interface of activated Arp3 with the first actin subunit of the new filament, and its central repeats extend along successive daughter-filament subunits. The preference of cortactin for activated Arp3 explains its retention at the actin branch and accounts for its synergy with other nucleation-promoting factors in regulating branched actin network dynamics.
History
DepositionJun 5, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17555.png

Downloads & links

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Map

FileDownload / File: emd_17555.map.gz / Format: CCP4 / Size: 325 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.)
1.07 Å/pix.
x 440 pix.
= 469.48 Å		1.07 Å/pix.
x 440 pix.
= 469.48 Å		1.07 Å/pix.
x 440 pix.
= 469.48 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.138
Minimum - Maximum-0.3135444 - 0.81058663
Average (Standard dev.)0.0011272142 (±0.018108143)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 469.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17555_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17555_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cortactin-stabilized Arp2/3-complex nucleated actin branches

EntireName: Cortactin-stabilized Arp2/3-complex nucleated actin branches
Components
  • Complex: Cortactin-stabilized Arp2/3-complex nucleated actin branches

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Supramolecule #1: Cortactin-stabilized Arp2/3-complex nucleated actin branches

SupramoleculeName: Cortactin-stabilized Arp2/3-complex nucleated actin branches
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)

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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
Details: 20 mM HEPES pH 7.5, 50mM KCl, 1mM EGTA, 1mM MgCl2, 0.2 mM ATP and 1 mM DTT
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 295.15 K / Instrument: LEICA EM GP / Details: Back blotting.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2001580
Startup modelType of model: NONE / Details: CryoSPARC ab-intio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 179923
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: OTHER

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