Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000439
UniProt IDQ13137
Primary gene name(s)CALCOCO2
Synonym gene name(s)NDP52
Protein nameCalcium-binding and coiled-coil domain-containing protein 2
Protein functionXenophagy-specific receptor required for autophagy-mediated intracellular bacteria degradation. Acts as an effector protein of galectin-sensed membrane damage that restricts the proliferation of infecting pathogens such as Salmonella typhimurium upon entry into the cytosol by targeting galectin-8-associated bacteria for autophagy, PubMed:22246324. Initially orchestrates bacteria targeting to autophagosomes and subsequently ensures pathogen degradation by regulating pathogen-containing autophagosome maturation, PubMed:23022382, PubMed:25771791. Bacteria targeting to autophagosomes relies on its interaction with MAP1LC3A, MAP1LC3B and/or GABARAPL2, whereas regulation of pathogen-containing autophagosome maturation requires the interaction with MAP3LC3C, PubMed:23022382, PubMed:25771791. May play a role in ruffle formation and actin cytoskeleton organization and seems to negatively regulate constitutive secretion, PubMed:17635994. {ECO:0000269|PubMed:17635994, ECO:0000269|PubMed:22246324, ECO:0000269|PubMed:23022382, ECO:0000269|PubMed:23386746, ECO:0000269|PubMed:25771791}.
Subcellular locationCytoplasm, perinuclear region {ECO:0000269|PubMed:12869526, ECO:0000269|PubMed:17635994, ECO:0000269|PubMed:9230084}. Cytoplasm, cytoskeleton {ECO:0000269|PubMed:17635994}. Cytoplasmic vesicle, autophagosome membrane {ECO:0000269|PubMed:25771791};
Peripheral membrane protein {ECO:0000305}. Note=According to PubMed:7540613, localizes to nuclear dots. According to PubMed:9230084 and PubMed:12869526, it is not a nuclear dot-associated protein but localizes predominantly in the cytoplasm with a coarse-grained distribution preferentially close to the nucleus. {ECO:0000269|PubMed:12869526, ECO:0000269|PubMed:7540613, ECO:0000269|PubMed:9230084}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q13137
Gene Ontology
(Biological Process)
Complete annatation
positive regulation of autophagosome maturation [GO:1901098];
response to interferon-gamma [GO:0034341];
viral process [GO:0016032];
xenophagy [GO:0098792]
Gene Ontology
(Molecular Function)
Complete annatation
protein homodimerization activity [GO:0042803]
Gene Ontology
(Cellular Component)
Complete annatation
autophagosome [GO:0005776];
autophagosome membrane [GO:0000421];
cytoplasm [GO:0005737];
cytoplasmic vesicle [GO:0031410];
cytoskeleton [GO:0005856];
intracellular membrane-bounded organelle [GO:0043231];
membrane [GO:0016020];
nucleus [GO:0005634];
perinuclear region of cytoplasm [GO:0048471]
Protein-protein interaction115535
Phylogenetic treeQ13137
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. CD3-1.200098039699880.0002975152696603760.0012610096018901
AZA vs. DISU0.1033659234696780.6824896616262620.966539755670263
AZA vs. IL70.008364601165570160.9652624774511520.999311006273513
AZA vs. SAHA-0.04531486911491670.8530730585078650.96562463647575
DISU vs. CD31.291311367003370.0004495078167130460.00208360419100014
DISU vs. IL7-0.1044251042652420.6781070081876130.912882938777306
DISU vs. SAHA-0.1469991892077550.6155986918208460.879068399131322
DMSO vs. AZA-0.02127746929828180.8988283229053751
DMSO vs. CD31.16974630316750.00030260025567530.0011968161858095
DMSO vs. DISU-0.1258184889252320.6057556733256580.939289650701039
DMSO vs. IL70.03651788788547050.8389183554183830.96460411742993
DMSO vs. SAHA-0.03098667402036420.8956974740216690.97487229226407
HIV vs. Mock in Activation-0.152975038041720.805908837436710.999983755607037
HIV vs. Mock in Latency-0.01822641049350120.9120956826378130.999834320637052
IL7 vs. CD31.215461871615870.000189642245451260.00101906508580636
SAHA vs. CD31.130411275623220.001621880608678850.00541345310582287
SAHA vs. IL7-0.05651331513351680.8173405407816080.921292110729731
(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) TRUE
(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 0.128311 0.406629
(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
0.611 1.218 0.911 0.909 1.051
(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
2MXP NMR - A=414-446.
3VVV X-ray 1.3Å A=21-141.
3VVW X-ray 2.5Å A=21-141.
4GXL X-ray 2.0Å B=368-381.
4HAN X-ray 2.5Å C/D=372-385.
4XKL X-ray 2.1Å B/D=414-446.
5AAQ NMR - A=388-446.

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

not found

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found