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VIM
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 1GK4, 1GK6, 1GK7, 3G1E, 3KLT, 3S4R, 3SSU, 3SWK, 3TRT, 3UF1, 4MCY, 4MCZ, 4MD0, 4MD5, 4MDJ, 4YPC, 4YV3
Identifiers
Aliases	VIM, CTRCT30, HEL113, vimentin
External IDs	OMIM: 193060; MGI: 98932; HomoloGene: 2538; GeneCards: VIM; OMA:VIM - orthologs
Gene location (Human) Chr. Chromosome 10 (human) Band 10p13 Start 17,228,241 bp End 17,237,593 bp
Gene location (Mouse) Chr. Chromosome 2 (mouse) Band 2 A1|2 10.04 cM Start 13,578,738 bp End 13,587,637 bp
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in ventricular zone Descending thoracic aorta right coronary artery synovial membrane spinal ganglia popliteal artery tibial arteries decidua ascending aorta tibial nerve Top expressed in endothelial cell of lymphatic vessel left lung lobe dermis Gonadal ridge external carotid artery tunica media of zone of aorta stroma of bone marrow internal carotid artery ascending aorta semi-lunar valve More reference expression data BioGPS More reference expression data
Gene ontology Molecular function scaffold protein binding structural molecule activity structural constituent of cytoskeleton protein C-terminus binding protein binding structural constituent of eye lens identical protein binding double-stranded RNA binding keratin filament binding protein domain specific binding Cellular component cytoplasm cytosol cell projection focal adhesion plasma membrane peroxisome cell leading edge neuron projection extracellular exosome cytoskeleton intermediate filament extracellular matrix nucleus polysome nuclear matrix phagocytic vesicle ribonucleoprotein complex Biological process intermediate filament organization negative regulation of neuron projection development SMAD protein signal transduction astrocyte development intermediate filament-based process positive regulation of gene expression muscle filament sliding Bergmann glial cell differentiation viral process lens fiber cell development cytokine-mediated signaling pathway positive regulation of collagen biosynthetic process regulation of mRNA stability positive regulation of translation cellular response to lipopolysaccharide cellular response to muramyl dipeptide cellular response to interferon-gamma Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 7431 22352 Ensembl ENSG00000026025 ENSMUSG00000026728 UniProt P08670 P20152 RefSeq (mRNA) NM_003380 NM_011701 RefSeq (protein) NP_003371 NP_035831 Location (UCSC) Chr 10: 17.23 – 17.24 Mb Chr 2: 13.58 – 13.59 Mb PubMed search
Wikidata
View/Edit Human View/Edit Mouse

Vimentin is a structural protein that in humans is encoded by the VIM gene. Its name comes from the Latin vimentum which refers to an array of flexible rods.

Vimentin is a type III intermediate filament (IF) protein that is expressed in mesenchymal cells. IF proteins are found in all animal cells as well as bacteria. IF, along with tubulin-based microtubules and actin-based microfilaments, comprises the cytoskeleton. All IF proteins are expressed in a highly developmentally-regulated fashion; vimentin is the major cytoskeletal component of mesenchymal cells. Because of this, vimentin is often used as a marker of mesenchymally-derived cells or cells undergoing an epithelial-to-mesenchymal transition (EMT) during both normal development and metastatic progression.

Structure

A vimentin monomer, like all other intermediate filaments, has a central α-helical domain, capped on each end by non-helical amino (head) and carboxyl (tail) domains. Two monomers are likely co-translationally expressed in a way that facilitates their formation of a coiled-coil dimer, which is the basic subunit of vimentin assembly.

The α-helical sequences contain a pattern of hydrophobic amino acids that contribute to forming a "hydrophobic seal" on the surface of the helix. In addition, there is a periodic distribution of acidic and basic amino acids that seems to play an important role in stabilizing coiled-coil dimers. The spacing of the charged residues is optimal for ionic salt bridges, which allows for the stabilization of the α-helix structure. While this type of stabilization is intuitive for intrachain interactions, rather than interchain interactions, scientists have proposed that perhaps the switch from intrachain salt bridges formed by acidic and basic residues to the interchain ionic associations contributes to the assembly of the filament.

Function

Vimentin plays a significant role in supporting and anchoring the position of the organelles in the cytosol. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally.

The dynamic nature of vimentin is important when offering flexibility to the cell. Scientists found that vimentin provided cells with a resilience absent from the microtubule or actin filament networks, when under mechanical stress in vivo. Therefore, in general, it is accepted that vimentin is the cytoskeletal component responsible for maintaining cell integrity. (It was found that cells without vimentin are extremely delicate when disturbed with a micropuncture). Transgenic mice that lack vimentin appeared normal and did not show functional differences. It is possible that the microtubule network may have compensated for the absence of the intermediate network. This result supports an intimate interactions between microtubules and vimentin. Moreover, when microtubule depolymerizers were present, vimentin reorganization occurred, once again implying a relationship between the two systems. On the other hand, wounded mice that lack the vimentin gene heal slower than their wild type counterparts.

In essence, vimentin is responsible for maintaining cell shape, integrity of the cytoplasm, and stabilizing cytoskeletal interactions. Vimentin has been shown to eliminate toxic proteins in JUNQ and IPOD inclusion bodies in asymmetric division of mammalian cell lines.

Also, vimentin is found to control the transport of low-density lipoprotein, LDL, -derived cholesterol from a lysosome to the site of esterification. With the blocking of transport of LDL-derived cholesterol inside the cell, cells were found to store a much lower percentage of the lipoprotein than normal cells with vimentin. This dependence seems to be the first process of a biochemical function in any cell that depends on a cellular intermediate filament network. This type of dependence has ramifications on the adrenal cells, which rely on cholesteryl esters derived from LDL.

Vimentin plays a role in aggresome formation, where it forms a cage surrounding a core of aggregated protein.

Clinical significance

It has been used as a sarcoma tumor marker to identify mesenchyme.

Methylation of the vimentin gene has been established as a biomarker of colon cancer and this is being utilized in the development of fecal tests for colon cancer. Statistically significant levels of vimentin gene methylation have also been observed in certain upper gastrointestinal pathologies such as Barrett's esophagus, esophageal adenocarcinoma, and intestinal type gastric cancer. High levels of DNA methylation in the promoter region have also been associated with markedly decreased survival in hormone positive breast cancers. Downregulation of vimentin was identified in cystic variant of papillary thyroid carcinoma using a proteomic approach. See also Anti-citrullinated protein antibody for its use in diagnosis of rheumatoid arthritis.

Interactions

Vimentin has been shown to interact with:

• DSP
• MEN1
• MYST2
• PKN1
• PRKCI
• PLEC
• SPTAN1
• UPP1
• YWHAZ

The 3' UTR of Vimentin mRNA has been found to bind a 46kDa protein.

References

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19. Moinova, Helen (April 2012). "Aberrant Vimentin Methylation is Characteristic of Upper GI Pathologies". Cancer Epidemiology, Biomarkers & Prevention. 21 (4): 594–600. PMC 3454489.
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28. Ratnayake WS, Apostolatos CA, Apostolatos AH, Schutte RJ, Huynh MA, Ostrov DA, Acevedo-Duncan M (2018). "Oncogenic PKC-ι activates Vimentin during epithelial-mesenchymal transition in melanoma; a study based on PKC-ι and PKC-ζ specific inhibitors". Cell Adhes Migr. 0: 1–17. PMC 6363030.
29. Herrmann H, Wiche G (1987). "Plectin and IFAP-300K are homologous proteins binding to microtubule-associated proteins 1 and 2 and to the 240-kilodalton subunit of spectrin". J Biol Chem. 262 (3): 1320–5. PMID 3027087.
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31. Russell RL, Cao D, Zhang D, Handschumacher RE, Pizzorno G (2001). "Uridine phosphorylase association with vimentin. Intracellular distribution and localization". J Biol Chem. 276 (16): 13302–7. PMID 11278417.
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Further reading

• Snásel J, Pichová I (1997). "The cleavage of host cell proteins by HIV-1 protease". Folia Biol. (Praha). 42 (5): 227–30. PMID 8997639.
• Lake JA, Carr J, Feng F, et al. (2003). "The role of Vif during HIV-1 infection: interaction with novel host cellular factors". J Clin Virol. 26 (2): 143–52. PMID 12600646.

External links

• Vimentin Images

• Genes on human chromosome 10
• Cytoskeleton
• Cell biology
• Tumor markers