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- EMDB-27717: Cryogenic electron microscopy 3D map of human full-length monomer... -

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Basic information

Entry
Database: EMDB / ID: EMD-27717
TitleCryogenic electron microscopy 3D map of human full-length monomeric alpha-catenin
Map data
Sample
  • Complex: Monomeric alpha-catenin (residues 1-906)
    • Protein or peptide: alpha-catenin
KeywordsF-actin / cell-cell junction / CELL ADHESION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsRangarajan ES / Izard T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Commun Biol / Year: 2023
Title: Distinct inter-domain interactions of dimeric versus monomeric α-catenin link cell junctions to filaments.
Authors: Erumbi S Rangarajan / Emmanuel W Smith / Tina Izard /
Abstract: Attachment between cells is crucial for almost all aspects of the life of cells. These inter-cell adhesions are mediated by the binding of transmembrane cadherin receptors of one cell to cadherins of ...Attachment between cells is crucial for almost all aspects of the life of cells. These inter-cell adhesions are mediated by the binding of transmembrane cadherin receptors of one cell to cadherins of a neighboring cell. Inside the cell, cadherin binds β-catenin, which interacts with α-catenin. The transitioning of cells between migration and adhesion is modulated by α-catenin, which links cell junctions and the plasma membrane to the actin cytoskeleton. At cell junctions, a single β-catenin/α-catenin heterodimer slips along filamentous actin in the direction of cytoskeletal tension which unfolds clustered heterodimers to form catch bonds with F-actin. Outside cell junctions, α-catenin dimerizes and links the plasma membrane to F-actin. Under cytoskeletal tension, α-catenin unfolds and forms an asymmetric catch bond with F-actin. To understand the mechanism of this important α-catenin function, we determined the 2.7 Å cryogenic electron microscopy (cryoEM) structures of filamentous actin alone and bound to human dimeric α-catenin. Our structures provide mechanistic insights into the role of the α-catenin interdomain interactions in directing α-catenin function and suggest a bivalent mechanism. Further, our cryoEM structure of human monomeric α-catenin provides mechanistic insights into α-catenin autoinhibition. Collectively, our structures capture the initial α-catenin interaction with F-actin before the sensing of force, which is a crucial event in cell adhesion and human disease.
History
DepositionJul 27, 2022-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27717.png

Downloads & links

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Map

FileDownload / File: emd_27717.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.48 Å/pix.
x 180 pix.
= 266.4 Å		1.48 Å/pix.
x 180 pix.
= 266.4 Å		1.48 Å/pix.
x 180 pix.
= 266.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.5094465 - 2.311435
Average (Standard dev.)0.0003541947 (±0.033544786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 266.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27717_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_27717_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Monomeric alpha-catenin (residues 1-906)

EntireName: Monomeric alpha-catenin (residues 1-906)
Components
  • Complex: Monomeric alpha-catenin (residues 1-906)
    • Protein or peptide: alpha-catenin

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Supramolecule #1: Monomeric alpha-catenin (residues 1-906)

SupramoleculeName: Monomeric alpha-catenin (residues 1-906) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.3 KDa

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Macromolecule #1: alpha-catenin

MacromoleculeName: alpha-catenin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSMTAVH AGNINFKWDP KSLEIRTLAV ERLLEPLVTQ VTTLVNTNSK GPSNKKRGRS KKAHVLAASV EQATENFLEK GDKIAKESQF LKEELVAAVE DVRKQGDLMK AAAGEFADDP CSSVKRGNMV RAARALLSAV TRLLILADMA DVYKLLVQLK VVEDGILKLR ...String:
GPLGSMTAVH AGNINFKWDP KSLEIRTLAV ERLLEPLVTQ VTTLVNTNSK GPSNKKRGRS KKAHVLAASV EQATENFLEK GDKIAKESQF LKEELVAAVE DVRKQGDLMK AAAGEFADDP CSSVKRGNMV RAARALLSAV TRLLILADMA DVYKLLVQLK VVEDGILKLR NAGNEQDLGI QYKALKPEVD KLNIMAAKRQ QELKDVGHRD QMAAARGILQ KNVPILYTAS QACLQHPDVA AYKANRDLIY KQLQQAVTGI SNAAQATASD DASQHQGGGG GELAYALNNF DKQIIVDPLS FSEERFRPSL EERLESIISG AALMADSSCT RDDRRERIVA ECNAVRQALQ DLLSEYMGNA GRKERSDALN SAIDKMTKKT RDLRRQLRKA VMDHVSDSFL ETNVPLLVLI EAAKNGNEKE VKEYAQVFRE HANKLIEVAN LACSISNNEE GVKLVRMSAS QLEALCPQVI NAALALAAKP QSKLAQENMD LFKEQWEKQV RVLTDAVDDI TSIDDFLAVS ENHILEDVNK CVIALQEKDV DGLDRTAGAI RGRAARVIHV VTSEMDNYEP GVYTEKVLEA TKLLSNTVMP RFTEQVEAAV EALSSDPAQP MDENEFIDAS RLVYDGIRDI RKAVLMIRTP EELDDSDFET EDFDVRSRTS VQTEDDQLIA GQSARAIMAQ LPQEQKAKIA EQVASFQEEK SKLDAEVSKW DDSGNDIIVL AKQMCMIMME MTDFTRGKGP LKNTSDVISA AKKIAEAGSR MDKLGRTIAD HCPDSACKQD LLAYLQRIAL YCHQLNICSK VKAEVQNLGG ELVVSGVDSA MSLIQAAKNL MNAVVQTVKA SYVASTKYQK SQGMASLNLP AVSWKMKAPE KKPLVKREKQ DETQTKIKRA SQKKHVNPVQ ALSEFKAMDS I

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMTrisTris
0.2 mMTCEPtris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 294.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsPhase plate: OTHER / Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 0.1 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: OTHER
Details: M-domain and F-actin binding domain of AlphaFold model.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 154710
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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