Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0007820
UniProt IDP08670
Primary gene name(s)VIM
Synonym gene name(s)unknown
Protein nameVimentin
Protein functionVimentins 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. {ECO:0000269|PubMed:21746880}.; FUNCTION: Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2. {ECO:0000269|PubMed:21746880}.
Subcellular locationCytoplasm {ECO:0000269|PubMed:21465480}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P08670
Gene Ontology
(Biological Process)
Complete annatation
astrocyte development [GO:0014002];
Bergmann glial cell differentiation [GO:0060020];
intermediate filament organization [GO:0045109];
lens fiber cell development [GO:0070307];
movement of cell or subcellular component [GO:0006928];
muscle filament sliding [GO:0030049];
negative regulation of neuron projection development [GO:0010977];
positive regulation of gene expression [GO:0010628];
SMAD protein signal transduction [GO:0060395];
viral process [GO:0016032]
Gene Ontology
(Molecular Function)
Complete annatation
double-stranded RNA binding [GO:0003725];
glycoprotein binding [GO:0001948];
identical protein binding [GO:0042802];
keratin filament binding [GO:1990254];
protein C-terminus binding [GO:0008022];
scaffold protein binding [GO:0097110];
structural constituent of cytoskeleton [GO:0005200];
structural constituent of eye lens [GO:0005212]
Gene Ontology
(Cellular Component)
Complete annatation
cell leading edge [GO:0031252];
cytoplasm [GO:0005737];
cytoskeleton [GO:0005856];
cytosol [GO:0005829];
extracellular exosome [GO:0070062];
focal adhesion [GO:0005925];
intermediate filament [GO:0005882];
intermediate filament cytoskeleton [GO:0045111];
neuron projection [GO:0043005];
peroxisome [GO:0005777];
plasma membrane [GO:0005886]
Protein-protein interaction113272
Phylogenetic treeP08670
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
gene status
Lu et al., J. Virol., 2011
      Folds changes 8h: unknown; Folds changes 16h: unknown; Tested: unknown;
Schoggins JW and Rice CM, Curr. Opin. Virol., 2011
      Targeted viruses: unknown
      Viral life cycle: unknown
      Mechanism related to antiviral activity: unknown
Anti-viral restriction factor Liu et al., Retrovirology, 2011
      unknown (Triplicates)

Gene Expression Profile       top

            Up-regulated;            Down-regulated

For brief introduction to each study, please go to the help page.

Gene expression during HIV latency

(1). Mohammadi et al., PLoS Pathog., 2014

Differentially expressed transcripts (Pairwise) during latency and subsequent viral reactivation using several agents - Primary CD4+ T-cell based model

DMSO: Dimethyl suloxyde (negative control) - 0.0033% final
SAHA: Vorinostat (Histone deacetylase inhibitor) - 0.5 μM
CD3: TCR Stimulation by IL-2+ antiCD3/anti-CD28 antibodies
IL7: Interleukin-7 based stimulation
DISU: Disulfiram (alcohol dehydrogenase inhibitor) - 0.5 μM
AZA: 5-azacytidine (AZA; DNA methylation inhibitor) - 1 μM
Experimental Condition Log2 Fold Change P value Adjusted P value
AZA vs. CD3-1.518462130749685.44943309421786e-063.57725851899179e-05
AZA vs. DISU-0.3126117499321330.2155229204891170.803182072036389
AZA vs. IL70.06002325986363410.7541455964088720.999311006273513
AZA vs. SAHA-0.4300613592177670.07916178710718290.34973176402511
DISU vs. CD31.194089008367290.001128640699714190.00460810669217001
DISU vs. IL70.3633263685889630.149052093192230.502001855422891
DISU vs. SAHA-0.1156277244426130.6923960380107660.909285051911964
DMSO vs. AZA-0.0008748916114126750.9958096859185111
DMSO vs. CD31.506603683201213.8061026703673e-062.40717618510005e-05
DMSO vs. DISU0.3100663568236860.2028984808887920.717776976395015
DMSO vs. IL70.06814844815764640.7034943371048840.939092989626859
DMSO vs. SAHA-0.4351324689858470.06548248845807150.296260249729518
HIV vs. Mock in Activation0.05728276496318590.9265976661630660.999983755607037
HIV vs. Mock in Latency-0.03839876732510480.8150827950680150.999834320637052
IL7 vs. CD31.585317593792531.38331858456908e-061.31054437619169e-05
SAHA vs. CD31.064773962662410.002906640433198220.00894487876828612
SAHA vs. IL7-0.4929575711575730.04300635156738830.165799934405834
(2). Iglesias-Ussel et al., J. Virol., 2013

Up and Downregulated transcripts during Latency (Latently infected CD4+ T cells vs Uninfected)- Primary CD4+Tcell based model
Log2 Fold Change P Value
-0.4087 0.03183

Gene expression during HIV infection and replication

(1). Imbeault et al., PloS Pathog., 2012

Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells
Experiment type Log2 Fold Change P Value Adjusted P Value
Infected vs. Mock unknown unknown unknown
Infected vs. Bystander unknown unknown unknown
(2). Lefebvre et al., J. Virol., 2011

Transcriptome analysis of T-cell line (Sup T1)
Log2 Fold Change unknown
(3). Li et al., J. Immunol., 2013

Lymphatic tissue
Acute Fold Change Acute P Value Asymt Fold Change Asypt P Value AIDS Fold Change AIDS P Value
-1.7 0.014386964 -1.8 0.005747411 -1.4 0.232588978
(4). Chang et al., MBio., 2011

Transcriptome analysis of T-cell line (Sup T1)

Derived from Sherrill-Mix et al., BMC Retrovirol., 2015 cross validation
Up-regulated (True) unknown
(5). Sherrill-Mix et al., BMC Retrovirol., 2015

Deep RNA-seq analysis of primary human T cell infected with low passage HIV isolate HIV89.6 - Primary CD4+ T cell based
Test Status Log2 Fold Change P Value
OK 0.327917 0.0140372
(6). Rotger et al., PLoS Pathog., 2010

Genome-wide mRNA expression of CD4+ T cells from HIV-infected patient
(Genes differentially expressed (at adjusted p<0.01) according to the empirical Bayes approach)
Log2 Fold Change P Value
unknown unknown

Proteomic/Transcriptomics studies indicating differentially expressed genes mediated by HIV

(1). Greenwood et al., Elife, 2016

Activated (CD3/CD28) Primary human CD4+ T cells infected with pNL4-3-dE-EGFP. The table shows the complete (unfiltered) TMT (tandem mass tag)-based proteomic time course dataset
6 h 24 h 48 h 72 h RTi
0.984 1.132 0.928 0.754 0.972
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
unknown unknown unknown unknown unknown unknown unknown
(3). Hyrcza et al., J. Virolo., 2007

Primary human CD4+ and CD8+ T Cells
Affymetrix Prob ID Fold Change In CD8? Category
unknown unknown unknown unknown

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1GK4 X-ray 2.3Å A/B/C/D/E/F=328-411.
1GK6 X-ray 1.9Å A/B=385-412.
1GK7 X-ray 1.4Å A=102-138.
3G1E X-ray 1.8Å A/B=102-138.
3KLT X-ray 2.7Å A/B/C/D=263-334.
3S4R X-ray 2.4Å A/B=99-189.
3SSU X-ray 2.6Å A/B=99-189.
3SWK X-ray 1.7Å A/B=153-238.
3TRT X-ray 2.3Å A/B=261-335.
3UF1 X-ray 2.8Å A/B/C/D=144-251.
4MCY X-ray 2.3Å C=66-78.
4MCZ X-ray 2.4Å C=59-71.
4MD0 X-ray 2.1Å C=59-71.
4MD5 X-ray 1.6Å C=66-78.
4MDI X-ray 2.0Å C=66-78.
4MDJ X-ray 1.7Å C=66-78.
4YPC X-ray 1.4Å A=161-243.
4YV3 X-ray 2.0Å A/B/C=161-238.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

HIV Partner Interaction Type PubMed
Envelope surface glycoprotein gp120 complexes with 23125841
retropepsin cleaves 10491200
Gag-Pol complexes with 23125841
matrix upregulates 24736615
Vpr downregulates 23874603
Envelope surface glycoprotein gp120 decreases phosphorylation of 7842474
Vif co-localizes with 8523563
Pr55(Gag) complexes with 23125841
Vpr modulates 19655254
retropepsin degrades 1516138
Nef complexes with 23125841

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa05169 Epstein-Barr virus infection - Homo sapiens (human)
hsa05206 MicroRNAs in cancer - Homo sapiens (human)