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- EMDB-47194: F-actin binding interface of alpha-E-catenin ABD (cadherin-cateni... -

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Entry
Database: EMDB / ID: EMD-47194
TitleF-actin binding interface of alpha-E-catenin ABD (cadherin-catenin complex) and afadin
Map data
Sample
  • Complex: F-actin binding interface of alpha-E-catenin ABD (cadherin-catenin complex) and afadin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Catenin alpha-1
    • Protein or peptide: Afadin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsCytoskeleton / cell adhesion / STRUCTURAL PROTEIN
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
Catenin alpha-1 / Actin, alpha skeletal muscle / Afadin
Similarity search - Component
Biological speciesHomo sapiens (human) / Gallus gallus (chicken) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGong R / Reynolds MJ / Alushin GM
Funding support United States, 2 items
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, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47194.png

Downloads & links

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Map

FileDownload / File: emd_47194.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 448 pix.
= 461.44 Å		1.03 Å/pix.
x 448 pix.
= 461.44 Å		1.03 Å/pix.
x 448 pix.
= 461.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.19992006 - 0.33679548
Average (Standard dev.)0.0000319196 (±0.003376377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 461.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47194_msk_1.map
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Half map: #1

Fileemd_47194_half_map_1.map
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Half map: #2

Fileemd_47194_half_map_2.map
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Sample components

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Entire : F-actin binding interface of alpha-E-catenin ABD (cadherin-cateni...

EntireName: F-actin binding interface of alpha-E-catenin ABD (cadherin-catenin complex) and afadin
Components
  • Complex: F-actin binding interface of alpha-E-catenin ABD (cadherin-catenin complex) and afadin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Catenin alpha-1
    • Protein or peptide: Afadin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: F-actin binding interface of alpha-E-catenin ABD (cadherin-cateni...

SupramoleculeName: F-actin binding interface of alpha-E-catenin ABD (cadherin-catenin complex) and afadin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.4 kDa/nm

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (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

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Catenin alpha-1

MacromoleculeName: Catenin alpha-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 100.110078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTAVHAGNIN FKWDPKSLEI RTLAVERLLE PLVTQVTTLV NTNSKGPSNK KRGRSKKAHV LAASVEQATE NFLEKGDKIA KESQFLKEE LVVAVEDVRK QGDLMKSAAG EFADDPCSSV KRGNMVRAAR ALLSAVTRLL ILADMADVYK LLVQLKVVED G ILKLRNAG ...String:
MTAVHAGNIN FKWDPKSLEI RTLAVERLLE PLVTQVTTLV NTNSKGPSNK KRGRSKKAHV LAASVEQATE NFLEKGDKIA KESQFLKEE LVVAVEDVRK QGDLMKSAAG EFADDPCSSV KRGNMVRAAR ALLSAVTRLL ILADMADVYK LLVQLKVVED G ILKLRNAG NEQDLGIQYK ALKPEVDKLN IMAAKRQQEL KDVGNRDQMA AARGILQKNV PILYTASQAC LQHPDVAAYK AN RDLIYKQ LQQAVTGISN AAQATASDDA AQHQGGSGGE LAYALNNFDK QIIVDPLSFS EERFRPSLEE RLESIISGAA LGA DSSCTE DDRRERIVAE CNAVRQALQD LLSEYMGNAG RKERSDALNS AIDKMTKKTR DLRRQLRKAV MDHVSDSFLE TNVP LLVLI EAAKNGNEKE VKEYAQVFRE HANKLIEVAN LACSISNNEE GVKLVRMSAS QLEALCPQVI NAALALAAKP QSKLA QENM DLFKEQWEKQ VRVLTDAVDD ITSIDDFLAV SENHILEDVN KCVIALQEKD VDGLDRTAGA IRGRAAEVIH 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

UniProtKB: Catenin alpha-1

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Macromolecule #3: Afadin

MacromoleculeName: Afadin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.150164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SGTRELRGSA NQAGPQSAQV AAAEWKKREE HQRWYEKEKA RLEEERERKR REQERKLGQM RSQTLNPASF SPLATQAKPE KPSTLQRPQ ETVIRELQPQ QQPRTIERKD LQYITISKEE LSSGDSLSPD PWKRDAREKL EKQQQMHIVD MLSKEIHELQ N KVDRTAEE ...String:
SGTRELRGSA NQAGPQSAQV AAAEWKKREE HQRWYEKEKA RLEEERERKR REQERKLGQM RSQTLNPASF SPLATQAKPE KPSTLQRPQ ETVIRELQPQ QQPRTIERKD LQYITISKEE LSSGDSLSPD PWKRDAREKL EKQQQMHIVD MLSKEIHELQ N KVDRTAEE SDRLRKLMLE WQFQKRLQES KQKDEDDDEE EDDDVDTMLI MQRLEAERRA R

UniProtKB: Afadin

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / 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 #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / 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
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 61.26 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6upv


Details: Alpha-E-catenin ABD-F-actin complex
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99745
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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