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- EMDB-20843: Alpha-E-catenin ABD-F-actin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20843
TitleAlpha-E-catenin ABD-F-actin complex
Map data
Sample
  • Complex: alpha-E-catenin ABD-F-actin complex
    • Protein or peptide: Catenin alpha-1
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / Striated Muscle Contraction / cellular response to indole-3-methanol ...negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / Striated Muscle Contraction / cellular response to indole-3-methanol / vinculin binding / flotillin complex / negative regulation of cell motility / apical junction assembly / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / Adherens junctions interactions / catenin complex / negative regulation of protein localization to nucleus / axon regeneration / negative regulation of neuroblast proliferation / smoothened signaling pathway / establishment or maintenance of cell polarity / Myogenesis / odontogenesis of dentin-containing tooth / skeletal muscle thin filament assembly / striated muscle thin filament / intercalated disc / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / neuroblast proliferation / RHO GTPases activate IQGAPs / skeletal muscle fiber development / stress fiber / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / VEGFR2 mediated vascular permeability / integrin-mediated signaling pathway / actin filament / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein localization / beta-catenin binding / cell-cell adhesion / response to estrogen / male gonad development / cell-cell junction / actin filament binding / actin cytoskeleton / cell migration / lamellipodium / cell junction / hydrolase activity / cell adhesion / cadherin binding / intracellular membrane-bounded organelle / focal adhesion / structural molecule activity / RNA binding / ATP binding / identical protein binding / plasma membrane / cytosol
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 speciesHomo sapiens (human) / Chicken (chicken)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMei L / Alushin GM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)5DP5OD017885 United States
CitationJournal: Elife / Year: 2020
Title: Molecular mechanism for direct actin force-sensing by α-catenin.
Authors: Lin Mei / Santiago Espinosa de Los Reyes / Matthew J Reynolds / Rachel Leicher / Shixin Liu / Gregory M Alushin /
Abstract: The actin cytoskeleton mediates mechanical coupling between cells and their tissue microenvironments. The architecture and composition of actin networks are modulated by force; however, it is unclear ...The actin cytoskeleton mediates mechanical coupling between cells and their tissue microenvironments. The architecture and composition of actin networks are modulated by force; however, it is unclear how interactions between actin filaments (F-actin) and associated proteins are mechanically regulated. Here we employ both optical trapping and biochemical reconstitution with myosin motor proteins to show single piconewton forces applied solely to F-actin enhance binding by the human version of the essential cell-cell adhesion protein αE-catenin but not its homolog vinculin. Cryo-electron microscopy structures of both proteins bound to F-actin reveal unique rearrangements that facilitate their flexible C-termini refolding to engage distinct interfaces. Truncating α-catenin's C-terminus eliminates force-activated F-actin binding, and addition of this motif to vinculin confers force-activated binding, demonstrating that α-catenin's C-terminus is a modular detector of F-actin tension. Our studies establish that piconewton force on F-actin can enhance partner binding, which we propose mechanically regulates cellular adhesion through α-catenin.
History
DepositionOct 18, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseSep 30, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6upv
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20843.png

Downloads & links

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Map

FileDownload / File: emd_20843.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.10648739 - 0.22557251
Average (Standard dev.)0.003192276 (±0.017626036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin205156212
Dimensions96184100
Spacing10096184
CellA: 103.0 Å / B: 98.88 Å / C: 189.51999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z10096184
origin x/y/z0.0000.0000.000
length x/y/z103.00098.880189.520
α/β/γ90.00090.00090.000
start NX/NY/NZ212205156
NX/NY/NZ10096184
MAP C/R/S321
start NC/NR/NS156205212
NC/NR/NS18496100
D min/max/mean-0.1060.2260.003

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Supplemental data

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Mask #1

Fileemd_20843_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: B-factor sharpened, local resolution-filtered map

Fileemd_20843_additional_1.map
AnnotationB-factor sharpened, local resolution-filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unfiltered, unsharpened map

Fileemd_20843_additional_2.map
Annotationunfiltered, unsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_20843_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_20843_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : alpha-E-catenin ABD-F-actin complex

EntireName: alpha-E-catenin ABD-F-actin complex
Components
  • Complex: alpha-E-catenin ABD-F-actin complex
    • Protein or peptide: Catenin alpha-1
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: alpha-E-catenin ABD-F-actin complex

SupramoleculeName: alpha-E-catenin ABD-F-actin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Actin binding domain (residues 664-906) of alpha-E-catenin bound to F-actin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.5 kDa/nm

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Macromolecule #1: Catenin alpha-1

MacromoleculeName: Catenin alpha-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.206352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTAVHAGNIN FKWDPKSLEI RTLAVERLLE PLVTQVTTLV NTNSKGPSNK KRGRSKKAHV LAASVEQATE NFLEKGDKIA KESQFLKEE LVAAVEDVRK QGDLMKAAAG EFADDPCSSV KRGNMVRAAR ALLSAVTRLL ILADMADVYK LLVQLKVVED G ILKLRNAG ...String:
MTAVHAGNIN FKWDPKSLEI RTLAVERLLE PLVTQVTTLV NTNSKGPSNK KRGRSKKAHV LAASVEQATE NFLEKGDKIA KESQFLKEE LVAAVEDVRK QGDLMKAAAG EFADDPCSSV KRGNMVRAAR ALLSAVTRLL ILADMADVYK LLVQLKVVED G ILKLRNAG NEQDLGIQYK ALKPEVDKLN IMAAKRQQEL KDVGHRDQMA AARGILQKNV PILYTASQAC LQHPDVAAYK AN RDLIYKQ LQQAVTGISN AAQATASDDA SQHQGGGGGE LAYALNNFDK QIIVDPLSFS EERFRPSLEE RLESIISGAA LMA DSSCTR DDRRERIVAE CNAVRQALQD LLSEYMGNAG RKERSDALNS AIDKMTKKTR DLRRQLRKAV MDHVSDSFLE TNVP LLVLI EAAKNGNEKE VKEYAQVFRE HANKLIEVAN LACSISNNEE GVKLVRMSAS QLEALCPQVI NAALALAAKP QSKLA QENM DLFKEQWEKQ VRVLTDAVDD ITSIDDFLAV SENHILEDVN KCVIALQEKD VDGLDRTAGA IRGRAARVIH VVTSEM DNY EPGVYTEKVL EATKLLSNTV MPRFTEQVEA AVEALSSDPA QPMDENEFID ASRLVYDGIR DIRKAVLMIR TPEELDD SD FETEDFDVRS RTSVQTEDDQ LIAGQSARAI MAQLPQEQKA KIAEQVASFQ EEKSKLDAEV SKWDDSGNDI IVLAKQMC M IMMEMTDFTR GKGPLKNTSD VISAAKKIAE AGSRMDKLGR TIADHCPDSA CKQDLLAYLQ RIALYCHQLN ICSKVKAEV QNLGGELVVS GVDSAMSLIQ AAKNLMNAVV QTVKASYVAS TKYQKSQGMA SLNLPAVSWK MKAPEKKPLV KREKQDETQT KIKRASQKK HVNPVQALSE FKAMDSI

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Macromolecule #2: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Chicken (chicken)
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

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / 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: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Average exposure time: 10.0 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.03 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.88 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Details: Relion 3.0 / Number images used: 414486
CTF correctionSoftware - Name: CTFFIND (ver. 4.0)
Segment selectionNumber selected: 540533 / Software - Name: RELION (ver. 3.0) / Details: helical auto-picking
Startup modelType of model: EMDB MAP
EMDB ID:

7115

Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3j8a

chain_id: A

4igg

chain_id: B, residue_range: 664-906
Output model

PDB-6upv:
Alpha-E-catenin ABD-F-actin complex

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