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- EMDB-19562: Vimentin intermediate filament protofibril stoichiometry -

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Basic information

Entry
Database: EMDB / ID: EMD-19562
TitleVimentin intermediate filament protofibril stoichiometry
Map dataVimentin intermediate filament / STA
Sample
  • Complex: Vimentin intermediate filament
    • Protein or peptide: Vimentin
Keywordsvimentin / intermediate filament / cytoskeleton / STRUCTURAL PROTEIN
Function / homology
Function and homology information


keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament / microtubule organizing center ...keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament / microtubule organizing center / intermediate filament cytoskeleton / cell leading edge / Bergmann glial cell differentiation / positive regulation of collagen biosynthetic process / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / regulation of mRNA stability / Late endosomal microautophagy / structural constituent of cytoskeleton / nuclear matrix / Aggrephagy / cellular response to type II interferon / Chaperone Mediated Autophagy / peroxisome / neuron projection development / double-stranded RNA binding / negative regulation of neuron projection development / scaffold protein binding / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / molecular adaptor activity / cytoskeleton / axon / protein domain specific binding / focal adhesion / positive regulation of gene expression / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Intermediate filament head, DNA-binding domain / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 20.2 Å
AuthorsEibauer M / Medalia O
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_207453 Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Vimentin filaments integrate low-complexity domains in a complex helical structure.
Authors: Matthias Eibauer / Miriam S Weber / Rafael Kronenberg-Tenga / Charlie T Beales / Rajaa Boujemaa-Paterski / Yagmur Turgay / Suganya Sivagurunathan / Julia Kraxner / Sarah Köster / Robert D ...Authors: Matthias Eibauer / Miriam S Weber / Rafael Kronenberg-Tenga / Charlie T Beales / Rajaa Boujemaa-Paterski / Yagmur Turgay / Suganya Sivagurunathan / Julia Kraxner / Sarah Köster / Robert D Goldman / Ohad Medalia /
Abstract: Intermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their ...Intermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion-beam milling, cryo-electron microscopy and tomography to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, intertwined and flexible helical structure of 40 α-helices in cross-section, organized into five protofibrils. Surprisingly, the intrinsically disordered head domains form a fiber in the lumen of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking mechanical strength and stretchability.
History
DepositionFeb 5, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19562.png

Downloads & links

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Map

FileDownload / File: emd_19562.map.gz / Format: CCP4 / Size: 251 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVimentin intermediate filament / STA
Voxel sizeX=Y=Z: 8.84 Å
Density
Contour LevelBy AUTHOR: 0.78
Minimum - Maximum-1.5250305 - 2.3141472
Average (Standard dev.)0.015348067 (±0.29859444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions404040
Spacing404040
CellA=B=C: 353.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Vimentin intermediate filament / STA / half map 1

Fileemd_19562_half_map_1.map
AnnotationVimentin intermediate filament / STA / half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Vimentin intermediate filament / STA / half map 2

Fileemd_19562_half_map_2.map
AnnotationVimentin intermediate filament / STA / half 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 : Vimentin intermediate filament

EntireName: Vimentin intermediate filament
Components
  • Complex: Vimentin intermediate filament
    • Protein or peptide: Vimentin

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Supramolecule #1: Vimentin intermediate filament

SupramoleculeName: Vimentin intermediate filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56 kDa/nm

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Macromolecule #1: Vimentin

MacromoleculeName: Vimentin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSTRSVSSSS YRRMFGGPGT ASRPSSSRSY VTTSTRTYSL GSALRPSTSR SLYASSPGGV YATRSSAVRL RSSVPGVRLL QDSVDFSLAD AINTEFKNTR TNEKVELQEL NDRFANYIDK VRFLEQQNKI LLAELEQLKG QGKSRLGDLY EEEMRELRRQ VDQLTNDKAR ...String:
MSTRSVSSSS YRRMFGGPGT ASRPSSSRSY VTTSTRTYSL GSALRPSTSR SLYASSPGGV YATRSSAVRL RSSVPGVRLL QDSVDFSLAD AINTEFKNTR TNEKVELQEL NDRFANYIDK VRFLEQQNKI LLAELEQLKG QGKSRLGDLY EEEMRELRRQ VDQLTNDKAR VEVERDNLAE DIMRLREKLQ EEMLQREEAE NTLQSFRQDV DNASLARLDL ERKVESLQEE IAFLKKLHEE EIQELQAQIQ EQHVQIDVDV SKPDLTAALR DVRQQYESVA AKNLQEAEEW YKSKFADLSE AANRNNDALR QAKQESTEYR RQVQSLTCEV DALKGTNESL ERQMREMEEN FAVEAANYQD TIGRLQDEIQ NMKEEMARHL REYQDLLNVK MALDIEIATY RKLLEGEESR ISLPLPNFSS LNLRETNLDS LPLVDTHSKR TLLIKTVETR DGQVINETSQ HHDDLE

UniProtKB: Vimentin

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Detailsnative vimentin intermediate filaments

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 7 / Number images used: 14273 / Software - Name: crYOLO
Final 3D classificationSoftware - Name: RELION
Details: Subtomograms were projected using the APT pipeline (APT, actin polarity toolbox). Low quality subtomograms were excluded by multiple rounds of unsupervised 2D classification in RELION.
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 42.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 72 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 20.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number subtomograms used: 2371
FSC plot (resolution estimation)

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