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- EMDB-26772: Cryogenic electron microscopy 3D map of F-actin bound by human di... -

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Basic information

Entry
Database: EMDB / ID: EMD-26772
TitleCryogenic electron microscopy 3D map of F-actin bound by human dimeric alpha-catenin
Map dataCryoem map
Sample
  • Complex: dimeric alpha-catenin (residues 22-906) complexed with F-actin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Catenin alpha-1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
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 / gap junction assembly / epithelial cell-cell adhesion / zonula adherens / gamma-catenin binding / cellular response to indole-3-methanol / vinculin binding ...negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / gap junction assembly / epithelial cell-cell adhesion / zonula adherens / gamma-catenin binding / 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 / cytoskeletal motor activator activity / negative regulation of neuroblast proliferation / smoothened signaling pathway / establishment or maintenance of cell polarity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / Myogenesis / actin filament bundle / odontogenesis of dentin-containing tooth / filamentous actin / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / neuroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intercalated disc / RHO GTPases activate IQGAPs / skeletal muscle fiber development / stress fiber / ovarian follicle development / titin binding / extrinsic apoptotic signaling pathway in absence of ligand / actin filament polymerization / acrosomal vesicle / VEGFR2 mediated vascular permeability / filopodium / actin filament / integrin-mediated signaling pathway / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein localization / cell-cell adhesion / beta-catenin binding / response to estrogen / male gonad development / calcium-dependent protein binding / cell migration / actin filament binding / cell-cell junction / actin cytoskeleton / cell junction / lamellipodium / cell body / cell adhesion / hydrolase activity / cadherin binding / protein domain specific binding / focal adhesion / intracellular membrane-bounded organelle / calcium ion binding / positive regulation of gene expression / structural molecule activity / magnesium ion binding / RNA binding / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
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) / Oryctolagus cuniculus (rabbit)
Methodhelical reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsRangarajan ES / Smith EW / 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
DepositionApr 27, 2022-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26772.png

Downloads & links

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Map

FileDownload / File: emd_26772.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoem map
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.0629992 - 2.1485922
Average (Standard dev.)0.0002508447 (±0.04518077)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 391.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_26772_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_26772_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dimeric alpha-catenin (residues 22-906) complexed with F-actin

EntireName: dimeric alpha-catenin (residues 22-906) complexed with F-actin
Components
  • Complex: dimeric alpha-catenin (residues 22-906) complexed with F-actin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Catenin alpha-1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: dimeric alpha-catenin (residues 22-906) complexed with F-actin

SupramoleculeName: dimeric alpha-catenin (residues 22-906) complexed with F-actin
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 42.109973 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

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Macromolecule #2: Catenin alpha-1

MacromoleculeName: Catenin alpha-1 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.216031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPHMTLAVER LLEPLVTQVT TLVNTNSKGP SNKKRGRSKK AHVLAASVEQ ATENFLEKGD KIAKESQFLK EELVAAVEDV RKQGDLMKA AAGEFADDPC SSVKRGNMVR AARALLSAVT RLLILADMAD VYKLLVQLKV VEDGILKLRN AGNEQDLGIQ Y KALKPEVD ...String:
GPHMTLAVER LLEPLVTQVT TLVNTNSKGP SNKKRGRSKK AHVLAASVEQ ATENFLEKGD KIAKESQFLK EELVAAVEDV RKQGDLMKA AAGEFADDPC SSVKRGNMVR AARALLSAVT RLLILADMAD VYKLLVQLKV VEDGILKLRN AGNEQDLGIQ Y KALKPEVD KLNIMAAKRQ QELKDVGHRD QMAAARGILQ KNVPILYTAS QACLQHPDVA AYKANRDLIY KQLQQAVTGI SN AAQATAS DDASQHQGGG GGELAYALNN FDKQIIVDPL SFSEERFRPS LEERLESIIS GAALMADSSC TRDDRRERIV AEC NAVRQA LQDLLSEYMG NAGRKERSDA LNSAIDKMTK KTRDLRRQLR KAVMDHVSDS FLETNVPLLV LIEAAKNGNE KEVK EYAQV FREHANKLIE VANLACSISN NEEGVKLVRM SASQLEALCP QVINAALALA AKPQSKLAQE NMDLFKEQWE KQVRV LTDA VDDITSIDDF LAVSENHILE DVNKCVIALQ EKDVDGLDRT AGAIRGRAAR VIHVVTSEMD NYEPGVYTEK VLEATK LLS NTVMPRFTEQ VEAAVEALSS DPAQPMDENE FIDASRLVYD GIRDIRKAVL MIRTPEELDD SDFETEDFDV RSRTSVQ TE DDQLIAGQSA RAIMAQLPQE QKAKIAEQVA SFQEEKSKLD AEVSKWDDSG NDIIVLAKQM CMIMMEMTDF TRGKGPLK N TSDVISAAKK IAEAGSRMDK LGRTIADHCP DSACKQDLLA YLQRIALYCH QLNICSKVKA EVQNLGGELV VSGVDSAMS LIQAAKNLMN AVVQTVKASY VASTKYQKSQ GMASLNLPAV SWKMKAPEKK PLVKREKQDE TQTKIKRASQ KKHVNPVQAL SEFKAMDSI

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 21 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chlorideSodium Chloride
20.0 mMTrisTris
1.0 mMDTTDithiothreitol
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 65 % / Chamber temperature: 294.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Specialist opticsPhase plate: OTHER / Energy filter - Name: In-column Omega Filter
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Average exposure time: 0.1 sec. / Average electron dose: 60.0 e/Å2

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Image processing

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

6upv

Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.5 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.7 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 403663
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6upv

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7utj:
Cryogenic electron microscopy 3D map of F-actin bound by human dimeric alpha-catenin

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