Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000945
UniProt IDQ96AY2
Primary gene name(s)EME1
Synonym gene name(s)MMS4
Protein nameCrossover junction endonuclease EME1
Protein functionInteracts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. May be required in mitosis for the processing of stalled or collapsed replication forks. {ECO:0000269|PubMed:12686547, ECO:0000269|PubMed:12721304, ECO:0000269|PubMed:14617801, ECO:0000269|PubMed:17289582}.
Subcellular locationNucleus, nucleolus {ECO:0000269|PubMed:14617801}. Note=Recruited to regions of DNA damage in S-phase cells.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q96AY2
Gene Ontology
(Biological Process)
Complete annatation
double-strand break repair [GO:0006302];
interstrand cross-link repair [GO:0036297];
intra-S DNA damage checkpoint [GO:0031573];
replication fork processing [GO:0031297];
resolution of meiotic recombination intermediates [GO:0000712];
response to intra-S DNA damage checkpoint signaling [GO:0072429]
Gene Ontology
(Molecular Function)
Complete annatation
DNA binding [GO:0003677];
endodeoxyribonuclease activity [GO:0004520];
metal ion binding [GO:0046872]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
nuclear heterochromatin [GO:0005720];
nucleolus [GO:0005730];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction127026
Phylogenetic treeQ96AY2
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
      unknown
Brass et al., Science, 2008
      unknown
Smith et al., J. Immunol, 2010
      unknown
Interferon-stimulated
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. CD31.800404673335990.05031358262479930.100400677521644
AZA vs. DISU0.2429985296610230.4093715969356750.908113198395223
AZA vs. IL70.2634644246666040.4198402670880540.999311006273513
AZA vs. SAHA-0.7956243540514510.06370303091758490.309246547684334
DISU vs. CD3-1.568401149076160.08507809327536210.164355655265002
DISU vs. IL70.01048261405280490.9728029855071330.996582747692222
DISU vs. SAHA-1.039273217418060.01264888960747570.120615639198034
DMSO vs. AZA-0.08736027390935680.7455026951652811
DMSO vs. CD3-1.899273996660390.03940397926668840.0787382451210134
DMSO vs. DISU-0.3323530390202130.2104199525845720.723648718724212
DMSO vs. IL70.3559243957632020.2074996439030880.716699329473652
DMSO vs. SAHA-0.7158679635642830.07028931378242720.309022826142054
HIV vs. Mock in Activation-0.1659040555071480.9242261752499030.999983755607037
HIV vs. Mock in Latency-0.05287497663985170.7902928769709910.999834320637052
IL7 vs. CD3-1.5243882747050.09650509177788290.184643468947452
SAHA vs. CD3-2.629041883266450.006020214070434180.0167203512792929
SAHA vs. IL7-1.065963495764170.01489998256336070.082696000427135
(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 0.817611 0.183631
(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

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
2ZIU X-ray 2.7Å B=246-570.
2ZIV X-ray 2.7Å B=246-367# B=403-570.
2ZIW X-ray 2.8Å B=246-570.
2ZIX X-ray 3.5Å B=246-570.
4P0P X-ray 2.8Å B=178-570.
4P0Q X-ray 2.8Å B=178-570.
4P0R X-ray 6.5Å B/D=178-570.
4P0S X-ray 6.0Å B/D/F/H=178-570.

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

HIV Partner Interaction Type PubMed
Vpr interacts with 25320300
25496524
Vpr induces phosphorylation of 24412650
24528857
24744753
25496524
Vpr complexes with 24412650
24528857
24795708
25496524

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03440 Homologous recombination - Homo sapiens (human)
hsa03460 Fanconi anemia pathway - Homo sapiens (human)
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