Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002790
UniProt IDP62314
Primary gene name(s)SNRPD1
Synonym gene name(s)unknown
Protein nameSmall nuclear ribonucleoprotein Sm D1
Protein functionCore component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins, snRNPs, the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA. {ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:23333303}.
Subcellular locationCytoplasm, cytosol {ECO:0000269|PubMed:18984161}. Nucleus {ECO:0000269|PubMed:18984161}. Note=SMN-mediated assembly into core snRNPs occurs in the cytosol before SMN-mediated transport to the nucleus to be included in spliceosomes.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P62314
Gene Ontology
(Biological Process)
Complete annatation
mRNA splicing, via spliceosome [GO:0000398];
nuclear import [GO:0051170];
RNA splicing [GO:0008380];
spliceosomal complex assembly [GO:0000245];
spliceosomal snRNP assembly [GO:0000387]
Gene Ontology
(Molecular Function)
Complete annatation
poly(A RNA binding [GO:0044822];
RNA binding [GO:0003723]
Gene Ontology
(Cellular Component)
Complete annatation
catalytic step 2 spliceosome [GO:0071013];
commitment complex [GO:0000243];
cytosol [GO:0005829];
methylosome [GO:0034709];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
pICln-Sm protein complex [GO:0034715];
precatalytic spliceosome [GO:0071011];
prespliceosome [GO:0071010];
small nuclear ribonucleoprotein complex [GO:0030532];
SMN-Sm protein complex [GO:0034719];
spliceosomal tri-snRNP complex [GO:0097526];
U12-type spliceosomal complex [GO:0005689];
U1 snRNP [GO:0005685];
U2 snRNP [GO:0005686];
U4 snRNP [GO:0005687];
U5 snRNP [GO:0005682]
Protein-protein interaction112516
Phylogenetic treeP62314
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. CD32.455932109100481.12443387934036e-122.70294536354352e-11
AZA vs. DISU-0.2878249529954420.2581965595870810.839581352451412
AZA vs. IL70.5200123288852380.007306006752543780.273634381687483
AZA vs. SAHA-0.3521057536276220.1518086940034240.496750710674391
DISU vs. CD3-2.755813879866291.14364073766637e-124.0278599251362e-11
DISU vs. IL70.7987262008936680.001694852021365210.0381361509195381
DISU vs. SAHA-0.06313695950012710.829070486833330.955499041613743
DMSO vs. AZA-0.1046252148765530.5370206640216421
DMSO vs. CD3-2.570355872857623.27515792264421e-148.98729582962387e-13
DMSO vs. DISU0.1817521013972540.4586807885734540.891797120862077
DMSO vs. IL70.6316467866523120.0005058869476949330.0351439895691296
DMSO vs. SAHA-0.2545863830457910.2831618831416880.6334470448016
HIV vs. Mock in Activation-0.1288777577098130.8358960900703560.999983755607037
HIV vs. Mock in Latency-0.1420792120280710.3966026647723510.999834320637052
IL7 vs. CD3-1.927749399918576.49861053858558e-091.00879049071164e-07
SAHA vs. CD3-2.832393427701317.30526750203353e-142.77305746235882e-12
SAHA vs. IL7-0.8747691416395170.0003828130594375480.00559701654506459
(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
1.9 0.000188815 1.4 0.021680644 1.4 0.136741481
(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
OK 0.107931 0.501544
(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
1.009 1.085 1.064 1.035 0.954
(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
1B34 X-ray 2.5Å A=1-119.
3CW1 X-ray 5.4Å B/M/N/O=1-119.
3JCR EM 7.0Å P/p=1-119.
3PGW X-ray 4.4Å U/X=1-119.
3S6N X-ray 2.5Å A=1-119.
4F7U X-ray 1.9Å A/C=1-119.
4PJO X-ray 3.3Å C/Q/c/q=2-85.
4V98 X-ray 3.1Å AA/AI/AQ/AY/Ag/Ao/Aw/BA/BI/BQ/BY/Bg/Bo/Bw/CA/CI/CQ/CY/Cg/Co=1-119.
4WZJ X-ray 3.6Å AB/AI/AP/BB/BI/BP/CB/CI/CP/DB/DI/DP=1-119.

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

HIV Partner Interaction Type PubMed
Tat stimulated by 11780068

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03040 Spliceosome - Homo sapiens (human)
hsa05322 Systemic lupus erythematosus - Homo sapiens (human)
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