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- EMDB-23030: Cryogenic electron microscopy model of full-length human metavinc... -

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Basic information

Entry
Database: EMDB / ID: EMD-23030
TitleCryogenic electron microscopy model of full-length human metavinculin H1'-parallel conformation 1
Map data
Sample
  • Complex: metavinculin
    • Protein or peptide: metavinculin
Keywordsactin / adaptor protein / cadherin / cancer / catenin / cell adhesion / cell junction / cell migration / cell signaling / focal adhesions / heart failure / inositol phospholipid / integrin / plasma membrane / skeletal muscle / smooth muscle
Function / homology
Function and homology information


regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding ...regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / apical junction assembly / costamere / adherens junction assembly / 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 / Smooth Muscle Contraction / cell-matrix adhesion / negative regulation of cell migration / cell projection / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / platelet aggregation / beta-catenin binding / 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 / Signaling by BRAF and RAF1 fusions / cell-cell junction / Signaling by ALK fusions and activated point mutants / extracellular vesicle / Platelet degranulation / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.15 Å
AuthorsIzard T / Rangarajan ES
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Int J Mol Sci / Year: 2021
Title: The Cryogenic Electron Microscopy Structure of the Cell Adhesion Regulator Metavinculin Reveals an Isoform-Specific Kinked Helix in Its Cytoskeleton Binding Domain.
Authors: Erumbi S Rangarajan / Tina Izard /
Abstract: Vinculin and its heart-specific splice variant metavinculin are key regulators of cell adhesion processes. These membrane-bound cytoskeletal proteins regulate the cell shape by binding to several ...Vinculin and its heart-specific splice variant metavinculin are key regulators of cell adhesion processes. These membrane-bound cytoskeletal proteins regulate the cell shape by binding to several other proteins at cell-cell and cell-matrix junctions. Vinculin and metavinculin link integrin adhesion molecules to the filamentous actin network. Loss of both proteins prevents cell adhesion and cell spreading and reduces the formation of stress fibers, focal adhesions, or lamellipodia extensions. The binding of talin at cell-matrix junctions or of α-catenin at cell-cell junctions activates vinculin and metavinculin by releasing their autoinhibitory head-tail interaction. Once activated, vinculin and metavinculin bind F-actin via their five-helix bundle tail domains. Unlike vinculin, metavinculin has a 68-amino-acid insertion before the second α-helix of this five-helix F-actin-binding domain. Here, we present the full-length cryogenic electron microscopy structure of metavinculin that captures the dynamics of its individual domains and unveiled a hallmark structural feature, namely a kinked isoform-specific α-helix in its F-actin-binding domain. Our identified conformational landscape of metavinculin suggests a structural priming mechanism that is consistent with the cell adhesion functions of metavinculin in response to mechanical and cellular cues. Our findings expand our understanding of metavinculin function in the heart with implications for the etiologies of cardiomyopathies.
History
DepositionNov 24, 2020-
Header (metadata) releaseJan 27, 2021-
Map releaseJan 27, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ktu
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23030.png

Downloads & links

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Map

FileDownload / File: emd_23030.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.18
Minimum - Maximum-0.411897 - 0.7961996
Average (Standard dev.)-0.0006263276 (±0.030524436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8250.8250.825
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z211.200211.200211.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.4120.796-0.001

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Supplemental data

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Sample components

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Entire : metavinculin

EntireName: metavinculin
Components
  • Complex: metavinculin
    • Protein or peptide: metavinculin

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Supramolecule #1: metavinculin

SupramoleculeName: metavinculin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: metavinculin

MacromoleculeName: metavinculin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 125.0615 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 VRKTPWYQHH HHHHHH

UniProtKB: Vinculin

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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

Concentration0.5 mg/mL
BufferpH: 8 / Details: 20 mM Tris, pH 8.0, 150 mM NaCl, 0.2 mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2998 / Average exposure time: 1.6 sec. / Average electron dose: 67.92 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 458305
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7ktu:
Cryogenic electron microscopy model of full-length human metavinculin H1'-parallel conformation 1

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