Details of Host Protein

 Host Protein General Information (ID: PT1060)
  Protein Name
Small nuclear ribonucleoprotein Sm D1 (SNRPD1)
  Gene Name
SNRPD1
  Host Species
Homo sapiens
  Uniprot Entry Name
SMD1_HUMAN
  Protein Families
SnRNP core protein family
  Subcellular Location
Cytoplasm; cytoso; Nucleus
  External Link
NCBI Gene ID
6632
Uniprot ID
P62314
Ensembl ID
ENSG00000167088
HGNC ID
HGNC:11158
  Function in Host
Plays a role in pre-mRNA splicing as a core component of thespliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Component of both the pre-catalytic spliceosome B complex and activatedspliceosome C complexes. Is also a componentof the minor U12 spliceosome. May act as a chargedprotein scaffold to promote snRNP assembly or strengthen snRNP-snRNPinteractions through non-specific electrostatic contacts with RNA. [1-10]
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  Related KEGG Pathway
Systemic lupus erythematosus hsa05322            Pathway Map 
Spliceosome hsa03040            Pathway Map 
  3D Structure
PDB ID: 1B34 
FASTA   Download
  2D PNG Download  
PDB File Download

Function of This Protein During Virus Infection
Virus NameSARS-COV-2 Protein Function Pro-viral [11]
Infected TissueLung Infection Time7-9 Days
Infected CellCalu-3 Cells (Human epithelial cell line) Cellosaurus IDCVCL_0609 
Method DescriptionTo detect the role of host protein SNRPD1 in viral infection, SNRPD1 protein knockout Calu-3 Cells were infected with SARS-COV-2 for 7 - 9 Days , and the effects on infection was detected through CRISPR-based genome-wide gene-knockout screen.
ResultsIt is reported that knockout of SNRPD1 leads to the decreased SARS-CoV-2 RNA levels compared with control group.

Host Protein - Virus RNA Network
  Network Download  

 Full List of Virus RNA Interacting with This Protien
            RNA Region: 3'-UTR (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [12]
              Strains Name
hCoV-19/Not Specified Virus Strain
              RNA Binding Region
3'-UTR
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line)  (CVCL_0336;CVCL_0609 )
              Cell Originated Tissue Liver; Lung
              Interaction Score P-value < 0.05
              Method Description RNA pull-down assays; liquid chromatography with tandem mass spectrometry (LC-MS/MS); Wilcoxon test; MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS)
           RNA Region: 5'-UTR (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [12]
              Strains Name
hCoV-19/Not Specified Virus Strain
              RNA Binding Region
5'-UTR
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line) Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line)  (CVCL_0336;CVCL_0609 )
              Cell Originated Tissue Liver; Lung
              Interaction Score P-value < 0.05
              Method Description RNA pull-down assays; liquid chromatography with tandem mass spectrometry (LC-MS/MS); Wilcoxon test; MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS)
           RNA Region: 5'-UTR-L (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [12]
              Strains Name
hCoV-19/Not Specified Virus Strain
              RNA Binding Region
5'-UTR-L
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line) Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line)  (CVCL_0336;CVCL_0609 )
              Cell Originated Tissue Liver; Lung
              Interaction Score P-value < 0.05
              Method Description RNA pull-down assays; liquid chromatography with tandem mass spectrometry (LC-MS/MS); Wilcoxon test; MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS)

Differential Gene Expression During SARS-COV-2 Infection
GEO Accession: GSE152641
Sample Type: Blood
Samples Details: Healthy Control: 24; COVID-19: 62
Platform: GPL24676 Illumina NovaSeq 6000
  PNG Download  
Picture Not Found

GEO Accession: GSE162835
Sample Type: Nasopharyngeal Swabs
Samples Details: COVID-19 (Mild Symptoms): 37; COVID-19 (Moderate Symptoms): 10; COVID-19 (Severe Symptoms): 3
Platform: GPL24676 Illumina NovaSeq 6000
  PNG Download  
Picture Not Found

GEO Accession: GSE175779
Sample Type: Human Bronchial Epithelial Cells
Samples Details: Healthy Control: 4 (0, 24, 48, 72 and 96 h); COVID-19: 4 (24, 48, 72 and 96 h)
Platform: GPL18573 Illumina NextSeq 500
  PNG Download  
Picture Not Found

Protein Sequence Information
MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR
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References
1 Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5 splice site recognition. Elife. 2015 Jan 2;4:e04986.
2 An Atomic Structure of the Human Spliceosome. Cell. 2017 May 18;169(5):918-929.e14.
3 Cryo-EM structure of a human spliceosome activated for step 2 of splicing. Nature. 2017 Feb 16;542(7641):318-323.
4 Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. Cell. 2017 Aug 10;170(4):701-713.e11.
5 Molecular architecture of the human U4/U6.U5 tri-snRNP. Science. 2016 Mar 25;351(6280):1416-20.
6 Structural basis of assembly chaperone- mediated snRNP formation. Mol Cell. 2013 Feb 21;49(4):692-703.
7 Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. Nature. 2009 Mar 26;458(7237):475-80.
8 An assembly chaperone collaborates with the SMN complex to generate spliceosomal SnRNPs. Cell. 2008 Oct 31;135(3):497-509.
9 The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. RNA. 2004 Jun;10(6):929-41.
10 Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. RNA. 2002 Apr;8(4):426-39.
11 Genome-wide CRISPR screens identify GATA6 as a proviral host factor for SARS-CoV-2 via modulation of ACE2. Nat Commun. 2022 Apr 25;13(1):2237.
12 Mapping the host protein interactome of non-coding regions in SARS-CoV-2 genome. bioRxiv. 2021 Jun; DOI:10.1101/2021.06.19.449092.