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- EMDB-10737: Actin filament structure from vinculin-induced bundles -

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Basic information

Entry
Database: EMDB / ID: EMD-10737
TitleActin filament structure from vinculin-induced bundles
Map dataActin filament structure from vinculin-induced bundles
Sample
  • Organelle or cellular component: Actin
    • Protein or peptide: Actin
Biological speciesOryctolagus cuniculus (rabbit)
Methodhelical reconstruction / cryo EM / Resolution: 14.2 Å
AuthorsBoujemaa-Paterski R / Martins B / Eibauer M / Geiger B / Medalia O
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179418 Switzerland
CitationJournal: Elife / Year: 2020
Title: Talin-activated vinculin interacts with branched actin networks to initiate bundles.
Authors: Rajaa Boujemaa-Paterski / Bruno Martins / Matthias Eibauer / Charlie T Beales / Benjamin Geiger / Ohad Medalia /
Abstract: Vinculin plays a fundamental role in integrin-mediated cell adhesion. Activated by talin, it interacts with diverse adhesome components, enabling mechanical coupling between the actin cytoskeleton ...Vinculin plays a fundamental role in integrin-mediated cell adhesion. Activated by talin, it interacts with diverse adhesome components, enabling mechanical coupling between the actin cytoskeleton and the extracellular matrix. Here we studied the interactions of activated full-length vinculin with actin and the way it regulates the organization and dynamics of the Arp2/3 complex-mediated branched actin network. Through a combination of surface patterning and light microscopy experiments we show that vinculin can bundle dendritic actin networks through rapid binding and filament crosslinking. We show that vinculin promotes stable but flexible actin bundles having a mixed-polarity organization, as confirmed by cryo-electron tomography. Adhesion-like synthetic design of vinculin activation by surface-bound talin revealed that clustered vinculin can initiate and immobilize bundles from mobile Arp2/3-branched networks. Our results provide a molecular basis for coordinate actin bundle formation at nascent adhesions.
History
DepositionMar 9, 2020-
Header (metadata) releaseMar 18, 2020-
Map releaseMar 18, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10737.png

Downloads & links

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Map

FileDownload / File: emd_10737.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationActin filament structure from vinculin-induced bundles
Voxel sizeX=Y=Z: 3.443 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.039152224 - 0.08623947
Average (Standard dev.)0.00012344639 (±0.0054111355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 495.79202 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.4433.4433.443
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z495.792495.792495.792
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.0390.0860.000

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Supplemental data

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Sample components

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Entire : Actin

EntireName: Actin
Components
  • Organelle or cellular component: Actin
    • Protein or peptide: Actin

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Supramolecule #1: Actin

SupramoleculeName: Actin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTL KYPIEHGIIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE K MTQIMFET FNVPAMYVAI QAVLSLYASG RTTGIVLDSG DGVTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTL KYPIEHGIIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE K MTQIMFET FNVPAMYVAI QAVLSLYASG RTTGIVLDSG DGVTHNVPIY EGYALPHAIM RL DLAGRDL TDYLMKILTE RGYSFVTTAE REIVRDIKEK LCYVALDFEN EMATAASSSS LEK SYELPD GQVITIGNER FRCPETLFQP SFIGMESAGI HETTYNSIMK CDIDIRKDLY ANNV MSGGT TMYPGIADRM QKEITALAPS TMKIKIIAPP ERKYSVWIGG SILASLSTFQ QMWIT KQEY DEAGPSIVHR KCF

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 3.5 µm / Nominal magnification: 14522
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 1.2 sec. / Average electron dose: 1.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 39231 / Software - Name: MATLAB (ver. 1.6.0)
CTF correctionSoftware - Name: TOM Toolbox
Startup modelType of model: OTHER / Details: Cylinder with diameter 80 A
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.7 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 14.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 29643

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