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- EMDB-21925: Structural basis of alphaE-catenin - F-actin catch bond behavior -

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Basic information

Entry
Database: EMDB / ID: EMD-21925
TitleStructural basis of alphaE-catenin - F-actin catch bond behavior
Map dataalphaE-catenin - F-actin catch bond behavior
Sample
  • Complex: Complex of alphaE-catenin actin binding domain with F-actin
    • Complex: Actin, alpha skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Catenin alpha-1
      • Protein or peptide: Catenin alpha-1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


negative regulation of integrin-mediated signaling pathway / VEGFR2 mediated vascular permeability / Adherens junctions interactions / RHO GTPases activate IQGAPs / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / cellular response to indole-3-methanol / vinculin binding ...negative regulation of integrin-mediated signaling pathway / VEGFR2 mediated vascular permeability / Adherens junctions interactions / RHO GTPases activate IQGAPs / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / cellular response to indole-3-methanol / vinculin binding / negative regulation of cell motility / flotillin complex / Myogenesis / apical junction assembly / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / catenin complex / negative regulation of protein localization to nucleus / axon regeneration / cytoskeletal motor activator activity / negative regulation of neuroblast proliferation / smoothened signaling pathway / establishment or maintenance of cell polarity / tropomyosin binding / myosin heavy chain binding / odontogenesis of dentin-containing tooth / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / intercalated disc / actin monomer binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / neuroblast proliferation / skeletal muscle fiber development / stress fiber / extrinsic apoptotic signaling pathway in absence of ligand / ovarian follicle development / titin binding / actin filament polymerization / acrosomal vesicle / filopodium / integrin-mediated signaling pathway / cell motility / actin filament / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / beta-catenin binding / cell-cell adhesion / response to estrogen / male gonad development / calcium-dependent protein binding / actin filament binding / cell-cell junction / protein localization / cell migration / actin cytoskeleton / lamellipodium / regulation of cell population proliferation / cell body / hydrolase activity / cadherin binding / protein domain specific binding / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / apoptotic process / structural molecule activity / magnesium ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Alpha-catenin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site ...Alpha-catenin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like 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
Catenin alpha-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Mus musculus (house mouse) / Rabbit (rabbit)
Methodhelical reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsXu XP / Pokutta S / Torres M / Swift MF / Hanein D / Volkmann N / Weis WI
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118326 United States
CitationJournal: Elife / Year: 2020
Title: Structural basis of αE-catenin-F-actin catch bond behavior.
Authors: Xiao-Ping Xu / Sabine Pokutta / Megan Torres / Mark F Swift / Dorit Hanein / Niels Volkmann / William I Weis /
Abstract: Cell-cell and cell-matrix junctions transmit mechanical forces during tissue morphogenesis and homeostasis. α-Catenin links cell-cell adhesion complexes to the actin cytoskeleton, and mechanical ...Cell-cell and cell-matrix junctions transmit mechanical forces during tissue morphogenesis and homeostasis. α-Catenin links cell-cell adhesion complexes to the actin cytoskeleton, and mechanical load strengthens its binding to F-actin in a direction-sensitive manner. Specifically, optical trap experiments revealed that force promotes a transition between weak and strong actin-bound states. Here, we describe the cryo-electron microscopy structure of the F-actin-bound αE-catenin actin-binding domain, which in solution forms a five-helix bundle. In the actin-bound structure, the first helix of the bundle dissociates and the remaining four helices and connecting loops rearrange to form the interface with actin. Deletion of the first helix produces strong actin binding in the absence of force, suggesting that the actin-bound structure corresponds to the strong state. Our analysis explains how mechanical force applied to αE-catenin or its homolog vinculin favors the strongly bound state, and the dependence of catch bond strength on the direction of applied force.
History
DepositionMay 6, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateOct 7, 2020-
Current statusOct 7, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wvt
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21925.png

Downloads & links

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Map

FileDownload / File: emd_21925.map.gz / Format: CCP4 / Size: 17.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationalphaE-catenin - F-actin catch bond behavior
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 165 pix.
= 170.775 Å		1.04 Å/pix.
x 165 pix.
= 170.775 Å		1.04 Å/pix.
x 165 pix.
= 170.775 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.035 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.6 / Movie #1: 1.6
Minimum - Maximum-7.761227 - 16.695711
Average (Standard dev.)-0.00000000935 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin212121
Dimensions165165165
Spacing165165165
CellA=B=C: 170.775 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0351.0351.035
M x/y/z165165165
origin x/y/z0.0000.0000.000
length x/y/z170.775170.775170.775
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS212121
NC/NR/NS165165165
D min/max/mean-7.76116.696-0.000

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Supplemental data

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Sample components

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Entire : Complex of alphaE-catenin actin binding domain with F-actin

EntireName: Complex of alphaE-catenin actin binding domain with F-actin
Components
  • Complex: Complex of alphaE-catenin actin binding domain with F-actin
    • Complex: Actin, alpha skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Catenin alpha-1
      • Protein or peptide: Catenin alpha-1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Complex of alphaE-catenin actin binding domain with F-actin

SupramoleculeName: Complex of alphaE-catenin actin binding domain with F-actin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Actin, alpha skeletal muscle

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

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Supramolecule #3: Catenin alpha-1

SupramoleculeName: Catenin alpha-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)

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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: Rabbit (rabbit)
Molecular weightTheoretical: 42.109973 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

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Macromolecule #2: Catenin alpha-1

MacromoleculeName: Catenin alpha-1 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.999281 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: AIMAQLPQEQ KAKIAEQVAS FQEEKSKLDA EVSKWDDSGN DIIVLAKQMC MIMMEMTDFT RGKGPLKNTS DVISAAKKIA EAGSRMDKL GRTIADHCPD SACKQDLLAY LQRIALYCHQ LNICSKVKAE VQNLGGELVV SGVDSAMSLI QAAKNLMNAV V QTVKASYV ...String:
AIMAQLPQEQ KAKIAEQVAS FQEEKSKLDA EVSKWDDSGN DIIVLAKQMC MIMMEMTDFT RGKGPLKNTS DVISAAKKIA EAGSRMDKL GRTIADHCPD SACKQDLLAY LQRIALYCHQ LNICSKVKAE VQNLGGELVV SGVDSAMSLI QAAKNLMNAV V QTVKASYV ASTKYQKSQG MASLNLPAVS WKMKAPEKKP LVKREKQDET QTKIKRASQK KHVNPVQALS EFKAMDSI

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 2-7 / Number grids imaged: 3 / Number real images: 5573 / Average exposure time: 1.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 422822
Segment selectionNumber selected: 728331
Startup modelType of model: OTHER
Details: in-house rabbit skeletal actin filament reconstruction filtered to 4 nm
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3)

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Atomic model buiding 1

Initial model(PDB ID:

6djo

,

6dv1

)
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6wvt:
Structural basis of alphaE-catenin - F-actin catch bond behavior

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