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- EMDB-15947: Direct observation of the open conformational state of formin mDi... -

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Entry
Database: EMDB / ID: EMD-15947
TitleDirect observation of the open conformational state of formin mDia1 at actin filament barbed end
Map dataActin barbed-end - Formin "Open State"
Sample
  • Complex: Actin barbed-end bound by formin mDia1 dimer in his "open state"
    • Organelle or cellular component: Formin mDia1 dimer
    • Organelle or cellular component: Alpha Actin subunits assembled in helicoidal F-actin filament
KeywordsActin binding protein / Complex / barbed-end / formin / MOTOR PROTEIN
Biological speciesMus musculus (house mouse) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / negative staining / Resolution: 26.0 Å
AuthorsMaufront J / Guichard B / Cao L / Di Cicco A / Jegou A / Romet-Lemonne G / Bertin A
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE11-0013-01 France
Citation
Journal: Mol Biol Cell / Year: 2023
Title: Direct observation of the conformational states of formin mDia1 at actin filament barbed ends and along the filament.
Authors: Julien Maufront / Bérengère Guichard / Lu-Yan Cao / Aurélie Di Cicco / Antoine Jégou / Guillaume Romet-Lemonne / Aurélie Bertin /
Abstract: The fine regulation of actin polymerization is essential to control cell motility and architecture and to perform essential cellular functions. Formins are key regulators of actin filament assembly, ...The fine regulation of actin polymerization is essential to control cell motility and architecture and to perform essential cellular functions. Formins are key regulators of actin filament assembly, known to processively elongate filament barbed ends and increase their polymerization rate. Different models have been extrapolated to describe the molecular mechanism governing the processive motion of formin FH2 domains at polymerizing barbed ends. Using negative stain electron microscopy, we directly identified for the first time two conformations of the mDia1 formin FH2 domains in interaction with the barbed ends of actin filaments. These conformations agree with the speculated open and closed conformations of the "stair-stepping" model. We observed the FH2 dimers to be in the open conformation for 79% of the data, interacting with the two terminal actin subunits of the barbed end while they interact with three actin subunits in the closed conformation. In addition, we identified and characterized the structure of single FH2 dimers encircling the core of actin filaments, and reveal their ability to spontaneously depart from barbed ends.
#1: Journal: BiorXiv / Year: 2022
Title: Direct observation of the open conformational state of formin mDia1 at actin filament barbed end
Authors: Maufront J / Bertin A
History
DepositionOct 11, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15947.png

Downloads & links

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Map

FileDownload / File: emd_15947.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationActin barbed-end - Formin "Open State"
Voxel sizeX=Y=Z: 2.13 Å
Density
Contour LevelBy AUTHOR: 0.0214
Minimum - Maximum-0.06896125 - 0.13171235
Average (Standard dev.)0.0005159779 (±0.0062722866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 383.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15947_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Actin barbed-end - Formin "Open State"

Fileemd_15947_half_map_1.map
AnnotationActin barbed-end - Formin "Open State"
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Actin barbed-end - Formin "Open State"

Fileemd_15947_half_map_2.map
AnnotationActin barbed-end - Formin "Open State"
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Actin barbed-end bound by formin mDia1 dimer in his "open state"

EntireName: Actin barbed-end bound by formin mDia1 dimer in his "open state"
Components
  • Complex: Actin barbed-end bound by formin mDia1 dimer in his "open state"
    • Organelle or cellular component: Formin mDia1 dimer
    • Organelle or cellular component: Alpha Actin subunits assembled in helicoidal F-actin filament

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Supramolecule #1: Actin barbed-end bound by formin mDia1 dimer in his "open state"

SupramoleculeName: Actin barbed-end bound by formin mDia1 dimer in his "open state"
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Formin mDia1 dimer

SupramoleculeName: Formin mDia1 dimer / type: organelle_or_cellular_component / ID: 2 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Alpha Actin subunits assembled in helicoidal F-actin filament

SupramoleculeName: Alpha Actin subunits assembled in helicoidal F-actin filament
type: organelle_or_cellular_component / ID: 3 / Parent: 1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation #1

Preparation ID1
Concentration0.04 mg/mL
BufferpH: 7.8
StainingType: NEGATIVE / Material: Uranyl Formate

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Sample preparation #2

Preparation ID2
Concentration0.01 mg/mL
BufferpH: 7.8
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 20.0 e/Å2

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Image processing

Particle selectionNumber selected: 20919
Startup modelType of model: INSILICO MODEL
In silico model: Structural models of a formin-bound barbed end in his open state and his closed state were generated within UCSF Chimera based on FH2-actin atomic structure PDB 1Y64 and actin ...In silico model: Structural models of a formin-bound barbed end in his open state and his closed state were generated within UCSF Chimera based on FH2-actin atomic structure PDB 1Y64 and actin filament atomic structure PDB 5OOE then low-pass filtered at 50 angstrom.
Details: Starting with a raw cylinder with an appropriate diameter converge to similar results.
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 3694
FSC plot (resolution estimation)

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