+Open data
-Basic information
Entry | Database: PDB / ID: 8rve | ||||||
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Title | Vimentin intermediate filament | ||||||
Components | Vimentin | ||||||
Keywords | STRUCTURAL PROTEIN / vimentin / intermediate filament / cytoskeleton | ||||||
Function / homology | Function and homology information lens fiber cell development / keratin filament binding / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center ...lens fiber cell development / keratin filament binding / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center / intermediate filament / cell leading edge / Bergmann glial cell differentiation / positive regulation of collagen biosynthetic process / Caspase-mediated cleavage of cytoskeletal proteins / regulation of mRNA stability / phagocytic vesicle / Late endosomal microautophagy / structural constituent of cytoskeleton / nuclear matrix / cellular response to type II interferon / Aggrephagy / Chaperone Mediated Autophagy / peroxisome / neuron projection development / double-stranded RNA binding / negative regulation of neuron projection development / scaffold protein binding / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / molecular adaptor activity / cytoskeleton / protein domain specific binding / axon / focal adhesion / positive regulation of gene expression / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7.2 Å | ||||||
Authors | Eibauer, M. / Medalia, O. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rve.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8rve.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8rve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rve_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 8rve_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8rve_validation.xml.gz | 268.4 KB | Display | |
Data in CIF | 8rve_validation.cif.gz | 449.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/8rve ftp://data.pdbj.org/pub/pdb/validation_reports/rv/8rve | HTTPS FTP |
-Related structure data
Related structure data | 16844MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 53722.582 Da / Num. of mol.: 78 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VIM / Production host: Escherichia coli (E. coli) / References: UniProt: P08670 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Vimentin intermediate filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 56 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 62 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 73.7308 ° / Axial rise/subunit: 42.461 Å / Axial symmetry: C1 | ||||||||||||||||||
Particle selection | Num. of particles selected: 1462717 | ||||||||||||||||||
3D reconstruction | Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236920 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL | ||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Details: PDBDEV_00000212 | ||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model |