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- EMDB-20844: Metavinculin ABD-F-actin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20844
TitleMetavinculin ABD-F-actin complex
Map data
Sample
  • Complex: metavinculin ABD-F-actin complex
    • Protein or peptide: Vinculin
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / Striated Muscle Contraction / dystroglycan binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / Striated Muscle Contraction / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / adherens junction assembly / apical junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / skeletal muscle thin filament assembly / striated muscle thin filament / Smooth Muscle Contraction / skeletal muscle fiber development / stress fiber / negative regulation of cell migration / cell-matrix adhesion / cell projection / morphogenesis of an epithelium / actin filament / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / beta-catenin binding / platelet aggregation / specific granule lumen / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / extracellular vesicle / Signaling by BRAF and RAF1 fusions / cell-cell junction / Signaling by ALK fusions and activated point mutants / Platelet degranulation / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / hydrolase activity / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Vinculin repeated domain signature. / Vinculin / 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. ...Vinculin repeated domain signature. / Vinculin / 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
Vinculin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human) / Chicken (chicken)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMei L / Alushin GM
Funding support United States, 1 items
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, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseSep 30, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6upw
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20844.png

Downloads & links

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Map

FileDownload / File: emd_20844.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.12548512 - 0.29957667
Average (Standard dev.)0.004031375 (±0.022539327)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin211153212
Dimensions10218680
Spacing80102186
CellA: 82.399994 Å / B: 105.06 Å / C: 191.58 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z80102186
origin x/y/z0.0000.0000.000
length x/y/z82.400105.060191.580
α/β/γ90.00090.00090.000
start NX/NY/NZ212211153
NX/NY/NZ80102186
MAP C/R/S321
start NC/NR/NS153211212
NC/NR/NS18610280
D min/max/mean-0.1250.3000.004

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Supplemental data

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Mask #1

Fileemd_20844_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unfiltered, unsharpened map

Fileemd_20844_additional_1.map
Annotationunfiltered, unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: B-factor sharpened, local resolution-filtered map

Fileemd_20844_additional_2.map
AnnotationB-factor sharpened, local resolution-filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_20844_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_20844_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : metavinculin ABD-F-actin complex

EntireName: metavinculin ABD-F-actin complex
Components
  • Complex: metavinculin ABD-F-actin complex
    • Protein or peptide: Vinculin
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: metavinculin ABD-F-actin complex

SupramoleculeName: metavinculin ABD-F-actin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.2 kDa/nm

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Macromolecule #1: Vinculin

MacromoleculeName: Vinculin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 123.956375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPVFHTRTIE SILEPVAQQI SHLVIMHEEG EVDGKAIPDL TAPVAAVQAA VSNLVRVGKE TVQTTEDQIL KRDMPPAFIK VENACTKLV QAAQMLQSDP YSVPARDYLI DGSRGILSGT SDLLLTFDEA EVRKIIRVCK GILEYLTVAE VVETMEDLVT Y TKNLGPGM ...String:
MPVFHTRTIE SILEPVAQQI SHLVIMHEEG EVDGKAIPDL TAPVAAVQAA VSNLVRVGKE TVQTTEDQIL KRDMPPAFIK VENACTKLV QAAQMLQSDP YSVPARDYLI DGSRGILSGT SDLLLTFDEA EVRKIIRVCK GILEYLTVAE VVETMEDLVT Y TKNLGPGM TKMAKMIDER QQELTHQEHR VMLVNSMNTV KELLPVLISA MKIFVTTKNS KNQGIEEALK NRNFTVEKMS AE INEIIRV LQLTSWDEDA WASKDTEAMK RALASIDSKL NQAKGWLRDP SASPGDAGEQ AIRQILDEAG KVGELCAGKE RRE ILGTCK MLGQMTDQVA DLRARGQGSS PVAMQKAQQV SQGLDVLTAK VENAARKLEA MTNSKQSIAK KIDAAQNWLA DPNG GPEGE EQIRGALAEA RKIAELCDDP KERDDILRSL GEISALTSKL ADLRRQGKGD SPEARALAKQ VATALQNLQT KTNRA VANS RPAKAAVHLE GKIEQAQRWI DNPTVDDRGV GQAAIRGLVA EGHRLANVMM GPYRQDLLAK CDRVDQLTAQ LADLAA RGE GESPQARALA SQLQDSLKDL KARMQEAMTQ EVSDVFSDTT TPIKLLAVAA TAPPDAPNRE EVFDERAANF ENHSGKL GA TAEKAAAVGT ANKSTVEGIQ ASVKTARELT PQVVSAARIL LRNPGNQAAY EHFETMKNQW IDNVEKMTGL VDEAIDTK S LLDASEEAIK KDLDKCKVAM ANIQPQMLVA GATSIARRAN RILLVAKREV ENSEDPKFRE AVKAASDELS KTISPMVMD AKAVAGNISD PGLQKSFLDS GYRILGAVAK VREAFQPQEP DFPPPPPDLE QLRLTDELAP PKPPLPEGEV PPPRPPPPEE KDEEFPEQK AGEVINQPMM MAARQLHDEA RKWSSKPGIP AAEVGIGVVA EADAADAAGF PVPPDMEDDY EPELLLMPSN Q PVNQPILA AAQSLHREAT KWSSKGNDII AAAKRMALLM AEMSRLVRGG SGTKRALIQC AKDIAKASDE VTRLAKEVAK QC TDKRIRT NLLQVCERIP TISTQLKILS TVKATMLGRT NISDEESEQA TEMLVHNAQN LMQSVKETVR EAEAASIKIR TDA GFTLRW VRKTPWYQ

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Macromolecule #2: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Chicken (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

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / 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
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.06 Å
Applied symmetry - Helical parameters - Δ&Phi: -167.07 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Details: Relion 3.0 / Number images used: 215369
CTF correctionSoftware - Name: CTFFIND (ver. 4.0)
Segment selectionNumber selected: 237503 / Software - Name: RELION (ver. 3.0) / Details: helical auto-picking
Startup modelType of model: EMDB MAP
EMDB ID:

7115

Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3j8a

chain_id: A

3jbk

chain_id: M
Output model

PDB-6upw:
Metavinculin ABD-F-actin complex

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