[English] 日本語
Yorodumi
- EMDB-6447: Cryo-EM reconstruction of the metavinculin-actin interface -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6447
TitleCryo-EM reconstruction of the metavinculin-actin interface
Map dataReconstruction of metavinculin tail domain bound to F-actin
Sample
  • Sample: Metavinculin tail domain bound to F-actin
  • Protein or peptide: skeletal muscle actin
  • Protein or peptide: Metavinculin tail domain, residues 858-1129
Keywordsactin / metavinculin / vinculin / cell migration / adhesion / mechanosensation / cytoskeleton
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 / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / costamere / apical junction assembly / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / cytoskeletal motor activator activity / regulation of focal adhesion assembly / maintenance of blood-brain barrier / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / brush border / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / Signaling by ALK fusions and activated point mutants / Smooth Muscle Contraction / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / cell-matrix adhesion / negative regulation of cell migration / filopodium / cell projection / actin filament / morphogenesis of an epithelium / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / sarcolemma / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / beta-catenin binding / specific granule lumen / calcium-dependent protein binding / Signaling by RAF1 mutants / extracellular vesicle / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / Platelet degranulation / lamellipodium / cell body / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / hydrolase activity / cell adhesion / cadherin binding / membrane raft / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / structural molecule activity / magnesium ion binding / protein-containing complex / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
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 speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsKim LY / Thompson PM / Lee HT / Pershad M / Campbell SL / Alushin GM
CitationJournal: J Mol Biol / Year: 2016
Title: The Structural Basis of Actin Organization by Vinculin and Metavinculin.
Authors: Laura Y Kim / Peter M Thompson / Hyunna T Lee / Mihir Pershad / Sharon L Campbell / Gregory M Alushin /
Abstract: Vinculin is an essential adhesion protein that links membrane-bound integrin and cadherin receptors through their intracellular binding partners to filamentous actin, facilitating mechanotransduction. ...Vinculin is an essential adhesion protein that links membrane-bound integrin and cadherin receptors through their intracellular binding partners to filamentous actin, facilitating mechanotransduction. Here we present an 8.5-Å-resolution cryo-electron microscopy reconstruction and pseudo-atomic model of the vinculin tail (Vt) domain bound to F-actin. Upon actin engagement, the N-terminal "strap" and helix 1 are displaced from the Vt helical bundle to mediate actin bundling. We find that an analogous conformational change also occurs in the H1' helix of the tail domain of metavinculin (MVt) upon actin binding, a muscle-specific splice isoform that suppresses actin bundling by Vt. These data support a model in which metavinculin tunes the actin bundling activity of vinculin in a tissue-specific manner, providing a mechanistic framework for understanding metavinculin mutations associated with hereditary cardiomyopathies.
History
DepositionSep 3, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseNov 4, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 6.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3jbk
  • Surface level: 6.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3jbk
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6447.png

Downloads & links

-
Map

FileDownload / File: emd_6447.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of metavinculin tail domain bound to F-actin
Voxel sizeX=Y=Z: 2.18 Å
Density
Contour LevelBy AUTHOR: 6.5 / Movie #1: 6.5
Minimum - Maximum-7.91757345 - 19.67712212
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-69-69-42
Dimensions200200200
Spacing200200200
CellA=B=C: 436.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.182.182.18
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z436.000436.000436.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-69-69-42
NC/NR/NS200200200
D min/max/mean-7.91819.6770.000

-
Supplemental data

-
Sample components

-
Entire : Metavinculin tail domain bound to F-actin

EntireName: Metavinculin tail domain bound to F-actin
Components
  • Sample: Metavinculin tail domain bound to F-actin
  • Protein or peptide: skeletal muscle actin
  • Protein or peptide: Metavinculin tail domain, residues 858-1129

-
Supramolecule #1000: Metavinculin tail domain bound to F-actin

SupramoleculeName: Metavinculin tail domain bound to F-actin / type: sample / ID: 1000
Details: Helical filament with one metavinculin tail domain bound per actin protomer
Oligomeric state: One metavinculin tail domain per actin protomer
Number unique components: 2

-
Macromolecule #1: skeletal muscle actin

MacromoleculeName: skeletal muscle actin / type: protein_or_peptide / ID: 1 / Name.synonym: actin / Oligomeric state: helical filament / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Muscle / Location in cell: Cytoplasm, cytoskeleton
Molecular weightTheoretical: 41.8 KDa
SequenceUniProtKB: Actin, alpha skeletal muscle

-
Macromolecule #2: Metavinculin tail domain, residues 858-1129

MacromoleculeName: Metavinculin tail domain, residues 858-1129 / type: protein_or_peptide / ID: 2 / Name.synonym: MVt / Oligomeric state: helical / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Focal adhesion / Location in cell: Cytoplasmic
Molecular weightTheoretical: 29.6 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3) / Recombinant plasmid: 2HR-T (Addgene #29718)
SequenceUniProtKB: Vinculin

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.0125 mg/mL
BufferpH: 7 / Details: 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM imidazole
GridDetails: 200 mesh 1.2 / 1.3 C-flat
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP
Method: 3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar MVt was then applied and incubated for 60 seconds. 3 ...Method: 3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar MVt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of MVt applied. After 60 seconds, 3 microliters of solution was removed, then the grid was blotted for 2 seconds before plunging.

-
Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 137615 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
DateSep 10, 2014
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 671 / Average electron dose: 25 e/Å2

-
Image processing

CTF correctionDetails: FREALIGN (per segment)
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.80 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.75 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: OTHER / Software - Name: CTFFIND3, EMAN2/SPARX, FREALIGN
DetailsMulti-model IHRSR was performed using EMAN2 / SPARX to select for bound segments, followed by single-model IHRSR with EMAN2 / SPARX and final reconstruction with FREALIGN (fixed helical parameters).

-
Atomic model buiding 1

Initial modelPDB ID:

1qkr


Chain - Chain ID: A
SoftwareName: Chimera, MDFF
DetailsComponents were initially rigid body fit using Chimera, followed by flexible fitting with MDFF.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3jbk:
Cryo-EM reconstruction of the metavinculin-actin interface

-
Atomic model buiding 2

Initial modelPDB ID:

3j8a


Chain - Chain ID: A
SoftwareName: MDFF
DetailsComponents were initially rigid body fit using Chimera, followed by flexible fitting with MDFF.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3jbk:
Cryo-EM reconstruction of the metavinculin-actin interface

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more