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

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Basic information

Entry
Database: PDB / ID: 6upv
TitleAlpha-E-catenin ABD-F-actin complex
Components
  • Actin, alpha skeletal muscle
  • Catenin alpha-1
KeywordsCELL ADHESION / alpha-catenin / catenin / actin / mechanobiology / mechanosensing / cytoskeleton
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 / flotillin complex / vinculin binding / catenin complex / apical junction assembly / negative regulation of cell motility / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / Adherens junctions interactions / negative regulation of protein localization to nucleus / axon regeneration / negative regulation of neuroblast proliferation / smoothened signaling pathway / Myogenesis / establishment or maintenance of cell polarity / odontogenesis of dentin-containing tooth / striated muscle thin filament / skeletal muscle thin filament assembly / intercalated disc / neuroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / RHO GTPases activate IQGAPs / ovarian follicle development / skeletal muscle fiber development / stress fiber / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / VEGFR2 mediated vascular permeability / integrin-mediated signaling pathway / actin filament / adherens junction / cell-cell adhesion / beta-catenin binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to estrogen / male gonad development / actin filament binding / cell-cell junction / cell junction / intracellular protein localization / cell migration / actin cytoskeleton / lamellipodium / hydrolase activity / cell adhesion / cadherin binding / focal adhesion / intracellular membrane-bounded organelle / structural molecule activity / Golgi apparatus / RNA binding / ATP binding / identical protein binding / nucleus / 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
ADENOSINE-5'-DIPHOSPHATE / Catenin alpha-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMei, L. / Alushin, G.M.
Funding support United States, 1items
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, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
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Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Apr 2, 2025Data content type: EM metadata
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Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: Catenin alpha-1
A: Actin, alpha skeletal muscle
L: Catenin alpha-1
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)412,04817
Polymers409,7917
Non-polymers2,25810
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, TIRF microscopy assays
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Catenin alpha-1 / Alpha E-catenin / Cadherin-associated protein / Renal carcinoma antigen NY-REN-13


Mass: 100206.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35221
#2: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41875.633 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P68139
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: alpha-E-catenin ABD-F-actin complex / Type: COMPLEX
Details: Actin binding domain (residues 664-906) of alpha-E-catenin bound to F-actin
Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 27.5 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Gallus gallus (chicken)9031
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 10 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.88 ° / Axial rise/subunit: 27.03 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 540533 / Details: helical auto-picking
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 414486 / Algorithm: FOURIER SPACE / Details: Relion 3.0 / Symmetry type: HELICAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDPdb chain residue range
13J8A

3j8a

A3J8A1
24IGG

4igg

B4IGG2664-906

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