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- PDB-9dva: F-actin binding interface of alpha-E-catenin ABD (cadherin-cateni... -

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Basic information

Entry
Database: PDB / ID: 9dva
TitleF-actin binding interface of alpha-E-catenin ABD (cadherin-catenin complex) and afadin
Components
  • Actin, alpha skeletal muscle
  • Afadin
  • Catenin alpha-1
KeywordsSTRUCTURAL PROTEIN / Cytoskeleton / cell adhesion
Function / homology
Function and homology information


regulation of oligodendrocyte progenitor proliferation / negative regulation of integrin-mediated signaling pathway / radial glial cell differentiation / adherens junction maintenance / establishment of protein localization to plasma membrane / VEGFR2 mediated vascular permeability / protein localization to cell junction / Adherens junctions interactions / RHO GTPases activate IQGAPs / pore complex assembly ...regulation of oligodendrocyte progenitor proliferation / negative regulation of integrin-mediated signaling pathway / radial glial cell differentiation / adherens junction maintenance / establishment of protein localization to plasma membrane / VEGFR2 mediated vascular permeability / protein localization to cell junction / Adherens junctions interactions / RHO GTPases activate IQGAPs / pore complex assembly / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / neuroepithelial cell differentiation / Striated Muscle Contraction / cellular response to indole-3-methanol / telencephalon development / flotillin complex / vinculin binding / negative regulation of cell motility / Myogenesis / cell-cell adhesion mediated by cadherin / catenin complex / apical junction assembly / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / brain morphogenesis / positive regulation of smoothened signaling pathway / negative regulation of protein localization to nucleus / axon regeneration / negative regulation of neuroblast proliferation / apical junction complex / smoothened signaling pathway / pore complex / establishment or maintenance of cell polarity / odontogenesis of dentin-containing tooth / regulation of postsynapse assembly / striated muscle thin filament / skeletal muscle thin filament assembly / homeostasis of number of cells / intercalated disc / neuroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / stress fiber / ovarian follicle development / skeletal muscle fiber development / extrinsic apoptotic signaling pathway in absence of ligand / cell adhesion molecule binding / presynaptic active zone membrane / hippocampal mossy fiber to CA3 synapse / acrosomal vesicle / integrin-mediated signaling pathway / adherens junction / actin filament / cell motility / postsynaptic density membrane / beta-catenin binding / cerebral cortex development / 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 junction / apical part of cell / protein localization / cell-cell junction / lamellipodium / actin cytoskeleton / regulation of cell population proliferation / hydrolase activity / cadherin binding / apoptotic process / negative regulation of apoptotic process / structural molecule activity / Golgi apparatus / signal transduction / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / Afadin, cargo binding domain / Alpha-catenin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Ras association (RalGDS/AF-6) domain / Vinculin/alpha-catenin / Vinculin family / Ras association (RalGDS/AF-6) domain / Dilute domain ...: / Afadin, cargo binding domain / Alpha-catenin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Ras association (RalGDS/AF-6) domain / Vinculin/alpha-catenin / Vinculin family / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Alpha-catenin/vinculin-like superfamily / Forkhead associated domain / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain 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 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / ATPase, nucleotide binding domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Catenin alpha-1 / Actin, alpha skeletal muscle / Afadin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGong, R. / Reynolds, M.J. / Alushin, G.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141044 United States
Other privateG-2020-14047
CitationJournal: bioRxiv / Year: 2024
Title: Afadin mediates cadherin-catenin complex clustering on F-actin linked to cooperative binding and filament curvature.
Authors: Rui Gong / Matthew J Reynolds / Xiaoyu Sun / Gregory M Alushin /
Abstract: The E-cadherin-β-catenin-αE-catenin (cadherin-catenin) complex couples the cytoskeletons of neighboring cells at adherens junctions (AJs) to mediate force transmission across epithelia. Mechanical ...The E-cadherin-β-catenin-αE-catenin (cadherin-catenin) complex couples the cytoskeletons of neighboring cells at adherens junctions (AJs) to mediate force transmission across epithelia. Mechanical force and auxiliary binding partners converge to stabilize the cadherin-catenin complex's inherently weak binding to actin filaments (F-actin) through unclear mechanisms. Here we show that afadin's coiled-coil (CC) domain and vinculin synergistically enhance the cadherin-catenin complex's F-actin engagement. The cryo-EM structure of an E-cadherin-β-catenin-αE-catenin-vinculin-afadin-CC supra-complex bound to F-actin reveals that afadin-CC bridges adjacent αE-catenin actin-binding domains along the filament, stabilizing flexible αE-catenin segments implicated in mechanical regulation. These cooperative binding contacts promote the formation of supra-complex clusters along F-actin. Additionally, cryo-EM variability analysis links supra-complex binding along individual F-actin strands to nanoscale filament curvature, a deformation mode associated with cytoskeletal forces. Collectively, this work elucidates a mechanistic framework by which vinculin and afadin tune cadherin-catenin complex-cytoskeleton coupling to support AJ function across varying mechanical regimes.
History
DepositionOct 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Catenin alpha-1
G: Afadin
H: Catenin alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)438,00618
Polymers435,7488
Non-polymers2,25810
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: 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
#2: Protein Catenin alpha-1 / 102 kDa cadherin-associated protein / CAP102 / Alpha E-catenin


Mass: 100110.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnna1, Catna1 / Production host: Homo sapiens (human) / References: UniProt: P26231
#3: Protein Afadin / Afadin adherens junction formation factor / Protein Af-6


Mass: 26150.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Afdn, Af6, Mllt4 / Production host: Homo sapiens (human) / References: UniProt: Q9QZQ1
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: F-actin binding interface of alpha-E-catenin ABD (cadherin-catenin complex) and afadin
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 5.4 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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 / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 61.26 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99745 / Symmetry type: POINT

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