Vimentin - Rattus norvegicus (Rat)

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P31000 (VIME_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 116. History...

Clusters with 100%, 90%, 50% identity |

Documents (1) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Vimentin

Gene names

Name:

Vim

Organism

Rattus norvegicus (Rat) [Reference proteome]

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	466 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally. Ref.6 Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2 By similarity. Ref.6
Subunit structure	Homopolymer assembled from elementary dimers. Interacts with LGSN and SYNM. Interacts (via rod region) with PLEC (via CH 1 domain). Interacts with SLC6A4 By similarity. Interacts with STK33 By similarity. Interacts with LARP6 By similarity. Interacts with RAB8B. Ref.7
Subcellular location	Nucleus matrix. Cytoplasm By similarity Ref.3.
Domain	The central alpha-helical coiled-coil rod region mediates elementary homodimerization By similarity.
Post-translational modification	One of the most prominent phosphoproteins in various cells of mesenchymal origin. Phosphorylation is enhanced during cell division, at which time vimentin filaments are significantly reorganized. Phosphorylation by PKN1 inhibit the formation of filaments By similarity. Filament disassembly during mitosis is promoted by phosphorylation at Ser-55 as well as by nestin Probable. Phosphorylated at Ser-56 by CDK5 during neutrophil secretion in the cytoplasm. Phosphorylated by STK33 By similarity. Ref.8
Sequence similarities	Belongs to the intermediate filament family.

Ontologies

Keywords
Cellular component	Cytoplasm Intermediate filament Nucleus
Domain	Coiled coil
PTM	Acetylation Phosphoprotein
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	aging Inferred from expression pattern PubMed 18077910. Source: RGD cellular response to fibroblast growth factor stimulus Inferred from expression pattern PubMed 15195687. Source: RGD decidualization Inferred from expression pattern PubMed 17653607. Source: RGD fat cell differentiation Inferred from expression pattern PubMed 8680470. Source: RGD positive regulation of glial cell proliferation Inferred from mutant phenotype PubMed 21250919. Source: RGD regulation of Schwann cell migration Inferred from direct assay PubMed 22371530. Source: RGD regulation of axonogenesis Inferred from direct assay PubMed 22371530. Source: RGD response to estradiol stimulus Inferred from expression pattern PubMed 21915674. Source: RGD response to radiation Inferred from expression pattern PubMed 17649822. Source: RGD response to selenium ion Inferred from expression pattern PubMed 22002783. Source: RGD response to vitamin D Inferred from expression pattern PubMed 18687349. Source: RGD response to zinc ion Inferred from expression pattern PubMed 22017769. Source: RGD skeletal muscle tissue regeneration Inferred from expression pattern PubMed 18941770. Source: RGD
Cellular_component	axon Inferred from direct assay PubMed 18431495. Source: RGD cell body Inferred from direct assay PubMed 7879923. Source: RGD cytosol Inferred from direct assay PubMed 10906761. Source: RGD nuclear matrix Inferred from electronic annotation. Source: UniProtKB-SubCell perinuclear region of cytoplasm Inferred from direct assay PubMed 21915674. Source: RGD type III intermediate filament Traceable author statement Ref.1. Source: RGD
Molecular_function	protein phosphatase 2A binding Inferred from direct assay PubMed 10906761. Source: RGD structural constituent of cytoskeleton Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed By similarity

Chain

2 – 466

465

Vimentin

PRO_0000063759

Regions

Region

2 – 95

Head

Region

96 – 407

312

Rod

Region

96 – 131

Coil 1A

Region

132 – 153

Linker 1

Region

154 – 245

Coil 1B

Region

246 – 268

Linker 12

Region

269 – 407

139

Coil 2

Region

408 – 466

Tail

Coiled coil

96 – 131

Coiled coil

154 – 245

Coiled coil

303 – 407

105

Sites

Site

351

Stutter By similarity

Amino acid modifications

Modified residue

N-acetylserine By similarity

Modified residue

Phosphoserine By similarity

Modified residue

Phosphoserine; by PKA and PKC By similarity

Modified residue

Phosphoserine By similarity

Modified residue

Phosphoserine; by PKC By similarity

Modified residue

Phosphoserine; by PKC By similarity

Modified residue

Phosphothreonine By similarity

Modified residue

Phosphoserine By similarity

Modified residue

Phosphoserine By similarity

Modified residue

Phosphoserine By similarity

Modified residue

Phosphoserine By similarity

Modified residue

Phosphothreonine By similarity

Modified residue

Phosphoserine By similarity

Modified residue

Phosphotyrosine By similarity

Modified residue

Phosphoserine; by CaMK2, PKA, PKC and ROCK2 By similarity

Modified residue

Phosphoserine; by PKC By similarity

Modified residue

Phosphoserine; by PKA By similarity

Modified residue

Phosphoserine By similarity

Modified residue

Phosphoserine; by PKA and PKC By similarity

Modified residue

Phosphotyrosine By similarity

Modified residue

Phosphoserine Probable

Modified residue

Phosphoserine; by CDK5 and CDK1 By similarity

Modified residue

Phosphotyrosine By similarity

Modified residue

Phosphoserine; by PKA and PKC By similarity

Modified residue

Phosphoserine; by AURKB and ROCK2 By similarity

Modified residue

Phosphoserine By similarity

Modified residue

Phosphoserine; by CaMK2 By similarity

Modified residue

104

N6-acetyllysine By similarity

Modified residue

117

Phosphotyrosine By similarity

Modified residue

120

N6-acetyllysine By similarity

Modified residue

139

N6-acetyllysine By similarity

Modified residue

144

Phosphoserine By similarity

Modified residue

214

Phosphoserine By similarity

Modified residue

226

Phosphoserine By similarity

Modified residue

261

Phosphoserine By similarity

Modified residue

266

Phosphothreonine By similarity

Modified residue

292

N6-acetyllysine By similarity

Modified residue

299

Phosphoserine By similarity

Modified residue

373

N6-acetyllysine By similarity

Modified residue

402

N6-acetyllysine By similarity

Modified residue

409

Phosphoserine By similarity

Modified residue

412

Phosphoserine By similarity

Modified residue

419

Phosphoserine By similarity

Modified residue

420

Phosphoserine By similarity

Modified residue

426

Phosphothreonine By similarity

Modified residue

430

Phosphoserine By similarity

Modified residue

436

Phosphothreonine By similarity

Modified residue

445

N6-acetyllysine By similarity

Modified residue

446

Phosphothreonine By similarity

Modified residue

458

Phosphothreonine By similarity

Modified residue

459

Phosphoserine By similarity

Experimental info

Mutagenesis

S → A: Retains filamentous network during mitosis when transfected alone and when coexpressed with nestin. Ref.8

Mutagenesis

458 – 459

TS → AA: Induces loss of filamentous network when coexpressed with nestin.

Sequences

Sequence

Length

Mass (Da)

Tools

P31000 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 501CDCD706166829
Show »

FASTA

466

53,733

        10         20         30         40         50         60 
MSTRSVSSSS YRRMFGGSGT SSRPSSNRSY VTTSTRTYSL GSALRPSTSR SLYSSSPGGA 

        70         80         90        100        110        120 
YVTRSSAVRL RSSMPGVRLL QDSVDFSLAD AINTEFKNTR TNEKVELQEL NDRFANYIDK 

       130        140        150        160        170        180 
VRFLEQQNKI LLAELEQLKG QGKSRLGDLY EEEMRELRRQ VDQLTNDKAR VEVERDNLAE 

       190        200        210        220        230        240 
DIMRLREKLQ EEMLQREEAE STLQSFRQDV DNASLARLDL ERKVESLQEE IAFLKKLHDE 

       250        260        270        280        290        300 
EIQELQAQIQ EQHVQIDVDV SKPDLTAALR DVRQQYESVA AKNLQEAEEW YKSKFADLSE 

       310        320        330        340        350        360 
AANRNNDALR QAKQESNEYR RQVQSLTCEV DALKGTNESL ERQMREMEEN FALEAANYQD 

       370        380        390        400        410        420 
TIGRLQDEIQ NMKEEMARHL REYQDLLNVK MALDIEIATY RKLLEGEESR ISLPLPNFSS 

       430        440        450        460 
LNLRETNLES LPLVDTHSKR TLLIKTVETR DGQVINETSQ HHDDLE

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Differential expression of vimentin in rat prostatic tumors." Bussemakers M.J.G., Verhaegh G.W.C.T., van Bokhoven A., Debruyne F.M.J., Schalken J.A. Biochem. Biophys. Res. Commun. 182:1254-1259(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: Fischer.
[2]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Prostate.
[3]	"Proteome analysis of a rat liver nuclear insoluble protein fraction and localization of a novel protein, ISP36, to compartments in the interchromatin space." Segawa M., Niino K., Mineki R., Kaga N., Murayama K., Sugimoto K., Watanabe Y., Furukawa K., Horigome T. FEBS J. 272:4327-4338(2005) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 37-50, SUBCELLULAR LOCATION. Tissue: Liver.
[4]	Lubec G., Afjehi-Sadat L., Kang S.U., Lubec S. Submitted (SEP-2007) to UniProtKB Cited for: PROTEIN SEQUENCE OF 51-64; 123-129; 223-235; 295-304; 321-341; 346-364; 391-401 AND 411-424, MASS SPECTROMETRY. Strain: Sprague-Dawley. Tissue: Brain and Spinal cord.
[5]	Paine M.L. Submitted (FEB-1992) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 86-160. Tissue: Mammary gland.
[6]	"The role of the vimentin intermediate filaments in rat 3Y1 cells elucidated by immunoelectron microscopy and computer-graphic reconstruction." Katsumoto T., Mitsushima A., Kurimura T. Biol. Cell 68:139-146(1990) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Rab8B GTPase and junction dynamics in the testis." Lau A.S., Mruk D.D. Endocrinology 144:1549-1563(2003) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RAB8B.
[8]	"Nestin promotes the phosphorylation-dependent disassembly of vimentin intermediate filaments during mitosis." Chou Y.-H., Khuon S., Herrmann H., Goldman R.D. Mol. Biol. Cell 14:1468-1478(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION AT SER-55, MUTAGENESIS OF SER-55 AND 458-THR-SER-459.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X62952 mRNA. Translation: CAA44722.1. BC061847 mRNA. Translation: AAH61847.1. M84481 mRNA. Translation: AAA42339.1.
IPI	IPI00230941.
PIR	S22119.
RefSeq	NP_112402.1. NM_031140.1.
UniGene	Rn.2710.
3D structure databases
ProteinModelPortal	P31000.
SMR	P31000. Positions 101-138, 328-406.
ModBase	Search...
Protein-protein interaction databases
IntAct	P31000. 5 interactions.
STRING	10116.ENSRNOP00000024430.
PTM databases
PhosphoSite	P31000.
Proteomic databases
PaxDb	P31000.
PRIDE	P31000.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	81818.
KEGG	rno:81818.
UCSC	RGD:621646. rat.
Organism-specific databases
CTD	7431.
RGD	621646. Vim.
Phylogenomic databases
eggNOG	NOG146769.
HOGENOM	HOG000230977.
HOVERGEN	HBG013015.
InParanoid	P31000.
KO	K07606.
OrthoDB	EOG4GHZPD.
Gene expression databases
Genevestigator	P31000.
GermOnline	ENSRNOG00000018087. Rattus norvegicus.
Family and domain databases
InterPro	IPR016044. F. IPR001664. IF. IPR006821. Intermed_filament_DNA-bd. IPR018039. Intermediate_filament_CS. [Graphical view]
PANTHER	PTHR23239. PTHR23239. 1 hit.
Pfam	PF00038. Filament. 1 hit. PF04732. Filament_head. 1 hit. [Graphical view]
PROSITE	PS00226. IF. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	615731.

Entry information

Entry name

VIME_RAT

Accession

Primary (citable) accession number: P31000

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 116 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents