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- PDB-8rve: Vimentin intermediate filament -

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Basic information

Entry
Database: PDB / ID: 8rve
TitleVimentin intermediate filament
ComponentsVimentin
KeywordsSTRUCTURAL PROTEIN / vimentin / intermediate filament / cytoskeleton
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsEibauer, M. / Medalia, O.
Funding support Switzerland, 1items
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 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Vimentin
1: Vimentin
2: Vimentin
3: Vimentin
4: Vimentin
5: Vimentin
6: Vimentin
7: Vimentin
8: Vimentin
9: Vimentin
A: Vimentin
AA: Vimentin
AB: Vimentin
AC: Vimentin
AD: Vimentin
AE: Vimentin
AF: Vimentin
AG: Vimentin
AH: Vimentin
AI: Vimentin
AJ: Vimentin
AK: Vimentin
AL: Vimentin
AM: Vimentin
AN: Vimentin
AO: Vimentin
AP: Vimentin
B: Vimentin
C: Vimentin
D: Vimentin
E: Vimentin
F: Vimentin
G: Vimentin
H: Vimentin
I: Vimentin
J: Vimentin
K: Vimentin
L: Vimentin
M: Vimentin
N: Vimentin
O: Vimentin
P: Vimentin
Q: Vimentin
R: Vimentin
S: Vimentin
T: Vimentin
U: Vimentin
V: Vimentin
W: Vimentin
X: Vimentin
Y: Vimentin
Z: Vimentin
a: Vimentin
b: Vimentin
c: Vimentin
d: Vimentin
e: Vimentin
f: Vimentin
g: Vimentin
h: Vimentin
i: Vimentin
j: Vimentin
k: Vimentin
l: Vimentin
m: Vimentin
n: Vimentin
o: Vimentin
p: Vimentin
q: Vimentin
r: Vimentin
s: Vimentin
t: Vimentin
u: Vimentin
v: Vimentin
w: Vimentin
x: Vimentin
y: Vimentin
z: Vimentin


Theoretical massNumber of molelcules
Total (without water)4,190,36178
Polymers4,190,36178
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Vimentin /


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Vimentin intermediate filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 56 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1crYOLOparticle selection
2EPUimage acquisition
4GctfCTF correction
7NAMDmodel fitting
12RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 73.7308 ° / Axial rise/subunit: 42.461 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 1462717
3D reconstructionResolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236920 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Details: PDBDEV_00000212
Atomic model buildingSource name: AlphaFold / Type: in silico model

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