Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000522
UniProt IDP15813
Primary gene name(s)CD1D
Synonym gene name(s)unknown
Protein nameAntigen-presenting glycoprotein CD1d
Protein functionAntigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells. {ECO:0000269|PubMed:17475845}.
Subcellular locationCell membrane {ECO:0000269|PubMed:11927549, ECO:0000269|PubMed:17475845, ECO:0000269|PubMed:9973405};
Single-pass type I membrane protein {ECO:0000305|PubMed:9973405}. Basolateral cell membrane {ECO:0000269|PubMed:9973405};
Single-pass type I membrane protein {ECO:0000305|PubMed:9973405}. Endosome membrane {ECO:0000269|PubMed:11927549, ECO:0000269|PubMed:9973405};
Single-pass type I membrane protein {ECO:0000305|PubMed:9973405}. Lysosome membrane {ECO:0000269|PubMed:17475845, ECO:0000269|PubMed:9973405};
Single-pass type I membrane protein {ECO:0000269|PubMed:9973405}. Endoplasmic reticulum membrane {ECO:0000269|PubMed:11927549};
Single-pass type I membrane protein {ECO:0000269|PubMed:11927549}. Note=Subject to intracellular trafficking between the cell membrane, endosomes and lysosomes. {ECO:0000269|PubMed:9973405}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P15813
Gene Ontology
(Biological Process)
Complete annatation
antigen processing and presentation, endogenous lipid antigen via MHC class Ib [GO:0048006];
antigen processing and presentation, exogenous lipid antigen via MHC class Ib [GO:0048007];
detection of bacterium [GO:0016045];
heterotypic cell-cell adhesion [GO:0034113];
innate immune response [GO:0045087];
positive regulation of innate immune response [GO:0045089];
positive regulation of T cell proliferation [GO:0042102];
regulation of immune response [GO:0050776];
T cell selection [GO:0045058];
viral process [GO:0016032]
Gene Ontology
(Molecular Function)
Complete annatation
beta-2-microglobulin binding [GO:0030881];
cell adhesion molecule binding [GO:0050839];
endogenous lipid antigen binding [GO:0030883];
exogenous lipid antigen binding [GO:0030884];
histone binding [GO:0042393];
lipid antigen binding [GO:0030882];
lipopeptide binding [GO:0071723];
receptor activity [GO:0004872]
Gene Ontology
(Cellular Component)
Complete annatation
basolateral plasma membrane [GO:0016323];
cell surface [GO:0009986];
cytoplasm [GO:0005737];
endoplasmic reticulum membrane [GO:0005789];
endosome membrane [GO:0010008];
integral component of plasma membrane [GO:0005887];
lysosomal membrane [GO:0005765];
plasma membrane [GO:0005886]
Protein-protein interaction107350
Phylogenetic treeP15813
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. CD3unknownunknownunknown
AZA vs. DISUunknownunknownunknown
AZA vs. IL7unknownunknownunknown
AZA vs. SAHAunknownunknownunknown
DISU vs. CD3unknownunknownunknown
DISU vs. IL7unknownunknownunknown
DISU vs. SAHAunknownunknownunknown
DMSO vs. AZAunknownunknownunknown
DMSO vs. CD3unknownunknownunknown
DMSO vs. DISUunknownunknownunknown
DMSO vs. IL7unknownunknownunknown
DMSO vs. SAHAunknownunknownunknown
HIV vs. Mock in Activationunknownunknownunknown
HIV vs. Mock in Latencyunknownunknownunknown
IL7 vs. CD3unknownunknownunknown
SAHA vs. CD3unknownunknownunknown
SAHA vs. IL7unknownunknownunknown
(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
unknown unknown

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
unknown unknown unknown unknown unknown unknown
(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) FALSE
(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
NOTEST 3.04503 1
(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
unknown unknown unknown unknown unknown
(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

Drugbank ID Drug Name Drug Status Pharmacological Action Drug Action
DB04661 Cis-tetracosenoyl sulfatide experimental unknown unknown

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1ZT4 X-ray 3.0Å A/C=19-299.
2PO6 X-ray 3.2Å A/E=24-295.
3HUJ X-ray 2.5Å A/C=21-295.
3SDX X-ray 3.1Å A/C=24-295.
3TZV X-ray 3.0Å C=21-295.
3U0P X-ray 2.8Å A/C/E=21-295.
3VWJ X-ray 3.0Å A=21-295.
3VWK X-ray 2.9Å A=21-295.
4EN3 X-ray 2.5Å C=21-295.
4LHU X-ray 2.8Å A=24-295.
4MNG X-ray 3.0Å A/C=21-201.
4MQ7 X-ray 2.6Å A=21-202.
4WO4 X-ray 2.5Å A=24-295.
4WW2 X-ray 2.4Å C=21-295.
4WWK X-ray 3.1Å C=21-295.

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

HIV Partner Interaction Type PubMed
Vpu inhibits 20530791
Envelope surface glycoprotein gp120 downregulates 15790518
Vpr downregulates 26116899
Nef inhibits 20530791
Nef downregulates 15916790
Vpu downregulates 20530791

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa04530 Tight junction - Homo sapiens (human)
hsa04640 Hematopoietic cell lineage - Homo sapiens (human)
hsa05146 Amoebiasis - Homo sapiens (human)