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Non-structural protein 1 (NS1) (NS1A)

 NS1_I72A2               Reviewed;         237 AA.
P03495; Q1K9D5;
21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
21-JUL-1986, sequence version 1.
30-AUG-2017, entry version 119.
RecName: Full=Non-structural protein 1 {ECO:0000255|HAMAP-Rule:MF_04066};
Short=NS1 {ECO:0000255|HAMAP-Rule:MF_04066};
AltName: Full=NS1A {ECO:0000255|HAMAP-Rule:MF_04066};
Name=NS {ECO:0000255|HAMAP-Rule:MF_04066};
Influenza A virus (strain A/Udorn/307/1972 H3N2).
Viruses; ssRNA viruses; ssRNA negative-strand viruses;
Orthomyxoviridae; Influenzavirus A.
NCBI_TaxID=381517;
NCBI_TaxID=8782; Aves.
NCBI_TaxID=9721; Cetacea (whales).
NCBI_TaxID=9606; Homo sapiens (Human).
NCBI_TaxID=9709; Phocidae (true seals).
NCBI_TaxID=9823; Sus scrofa (Pig).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
PubMed=7407920; DOI=10.1016/0092-8674(80)90484-5;
Lamb R.A., Lai C.-J.;
"Sequence of interrupted and uninterrupted mRNAs and cloned DNA coding
for the two overlapping nonstructural proteins of influenza virus.";
Cell 21:475-485(1980).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
Mbawuike I.N., Zhang Y., Yamada R.E., Nino D., Bui H.-H., Sette A.,
Couch R.B.;
"Complete genome sequencing and analysis of selected influenza virus
vaccine strains spanning six decades (1933-1999).";
Submitted (APR-2006) to the EMBL/GenBank/DDBJ databases.
[3]
MUTAGENESIS OF 7-SER-SER-8; 19-ARG-PHE-20; 31-PRO-PHE-32;
35-ARG--ARG-38; 39-ASP-GLN-40; 48-SER-THR-49; 62-LYS-GLN-63;
73-SER-ASP-74; 87-SER-ARG-88; 99-SER-ARG-100; 116-CYS-ILE-117;
134-PHE--VAL-136; LEU-141; LEU-144; LEU-146; 150-PHE-THR-151;
160-ILE-SER-161; 175-LYS-ASN-176; 199-GLN-ARG-200; 205-SER-SER-206 AND
219-LYS-LYS-221.
PubMed=8139028;
Qian X.Y., Alonso-Caplen F., Krug R.M.;
"Two functional domains of the influenza virus NS1 protein are
required for regulation of nuclear export of mRNA.";
J. Virol. 68:2433-2441(1994).
[4]
DIMERIZATION.
PubMed=7571411; DOI=10.1006/viro.1995.1499;
Nemeroff M.E., Qian X.Y., Krug R.M.;
"The influenza virus NS1 protein forms multimers in vitro and in
vivo.";
Virology 212:422-428(1995).
[5]
RNA-BINDING.
PubMed=8806538; DOI=10.1006/viro.1996.0453;
Wang W., Krug R.M.;
"The RNA-binding and effector domains of the viral NS1 protein are
conserved to different extents among influenza A and B viruses.";
Virology 223:41-50(1996).
[6]
FUNCTION, AND INTERACTION WITH HUMAN CPSF4.
PubMed=9651582; DOI=10.1016/S1097-2765(00)80099-4;
Nemeroff M.E., Barabino S.M.L., Li Y., Keller W., Krug R.M.;
"Influenza virus NS1 protein interacts with the cellular 30 kDa
subunit of CPSF and inhibits 3'end formation of cellular pre-mRNAs.";
Mol. Cell 1:991-1000(1998).
[7]
INTERACTION WITH HUMAN EIF2AK2/PKR.
PubMed=9781815; DOI=10.1089/jir.1998.18.757;
Tan S.L., Katze M.G.;
"Biochemical and genetic evidence for complex formation between the
influenza A virus NS1 protein and the interferon-induced PKR protein
kinase.";
J. Interferon Cytokine Res. 18:757-766(1998).
[8]
FUNCTION.
PubMed=9560194; DOI=10.1073/pnas.95.9.4864;
Li Y., Yamakita Y., Krug R.M.;
"Regulation of a nuclear export signal by an adjacent inhibitory
sequence: the effector domain of the influenza virus NS1 protein.";
Proc. Natl. Acad. Sci. U.S.A. 95:4864-4869(1998).
[9]
INTERACTION WITH HUMAN PABPN1.
PubMed=10205180; DOI=10.1093/emboj/18.8.2273;
Chen Z., Li Y., Krug R.M.;
"Influenza A virus NS1 protein targets poly(A)-binding protein II of
the cellular 3'-end processing machinery.";
EMBO J. 18:2273-2283(1999).
[10]
MUTAGENESIS OF 186-GLU-TRP-187; 201-PHE--TRP-203 AND 212-PRO-PRO-213.
PubMed=11421366; DOI=10.1017/S1355838201010226;
Li Y., Chen Z.Y., Wang W., Baker C.C., Krug R.M.;
"The 3'-end-processing factor CPSF is required for the splicing of
single-intron pre-mRNAs in vivo.";
RNA 7:920-931(2001).
[11]
REVIEW.
PubMed=12758165; DOI=10.1016/S0042-6822(03)00119-3;
Krug R.M., Yuan W., Noah D.L., Latham A.G.;
"Intracellular warfare between human influenza viruses and human
cells: the roles of the viral NS1 protein.";
Virology 309:181-189(2003).
[12]
FUNCTION, AND INTERACTION WITH HOST CPSF4.
PubMed=16571812; DOI=10.1128/JVI.80.8.3957-3965.2006;
Twu K.Y., Noah D.L., Rao P., Kuo R.L., Krug R.M.;
"The CPSF30 binding site on the NS1A protein of influenza A virus is a
potential antiviral target.";
J. Virol. 80:3957-3965(2006).
[13]
STRUCTURE BY NMR OF 1-73.
PubMed=9360601; DOI=10.1038/nsb1197-891;
Chien C.Y., Tejero R., Huang Y., Zimmerman D.E., Rios C.B., Krug R.M.,
Montelione G.T.;
"A novel RNA-binding motif in influenza A virus non-structural protein
1.";
Nat. Struct. Biol. 4:891-895(1997).
[14]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-72.
PubMed=9360602; DOI=10.1038/nsb1197-896;
Liu J., Lynch P.A., Chien C.Y., Montelione G.T., Krug R.M.,
Berman H.M.;
"Crystal structure of the unique RNA-binding domain of the influenza
virus NS1 protein.";
Nat. Struct. Biol. 4:896-899(1997).
-!- FUNCTION: Inhibits post-transcriptional processing of cellular
pre-mRNA, by binding and inhibiting two cellular proteins that are
required for the 3'-end processing of cellular pre-mRNAs: the 30
kDa cleavage and polyadenylation specificity factor/CPSF4 and the
poly(A)-binding protein 2/PABPN1. In turn, unprocessed 3' end pre-
mRNAs accumulate in the host nucleus and are no longer exported to
the cytoplasm. Cellular protein synthesis is thereby shut off very
early after virus infection. Viral protein synthesis is not
affected by the inhibition of the cellular 3' end processing
machinery because the poly(A) tails of viral mRNAs are produced by
the viral polymerase through a stuttering mechanism.
{ECO:0000255|HAMAP-Rule:MF_04066, ECO:0000269|PubMed:16571812,
ECO:0000269|PubMed:9560194, ECO:0000269|PubMed:9651582}.
-!- FUNCTION: Prevents the establishment of the cellular antiviral
state by inhibiting TRIM25-mediated DDX58 ubiquitination, which
normally triggers the antiviral transduction signal that leads to
the activation of type I IFN genes by transcription factors IRF3
and IRF7. Prevents human EIF2AK2/PKR activation, either by binding
double-strand RNA, or by interacting directly with EIF2AK2/PKR.
This function may be important at the very beginning of the
infection, when NS1 is mainly present in the cytoplasm. Also binds
poly(A) and U6 snRNA. {ECO:0000255|HAMAP-Rule:MF_04066}.
-!- SUBUNIT: Homodimer. Interacts with host TRIM25 (via coiled coil);
this interaction specifically inhibits TRIM25 multimerization and
TRIM25-mediated DDX58 CARD ubiquitination. Interacts with human
EIF2AK2/PKR, CPSF4, IVNS1ABP and PABPN1. {ECO:0000255|HAMAP-
Rule:MF_04066, ECO:0000269|PubMed:10205180,
ECO:0000269|PubMed:16571812, ECO:0000269|PubMed:9651582,
ECO:0000269|PubMed:9781815}.
-!- INTERACTION:
Q92934:BAD (xeno); NbExp=2; IntAct=EBI-2548993, EBI-700771;
O43521:BCL2L11 (xeno); NbExp=2; IntAct=EBI-2548993, EBI-526406;
O60869:EDF1 (xeno); NbExp=2; IntAct=EBI-2548993, EBI-781301;
Q13651:IL10RA (xeno); NbExp=2; IntAct=EBI-2548993, EBI-1031656;
P35568:IRS1 (xeno); NbExp=2; IntAct=EBI-2548993, EBI-517592;
Q9UBF8:PI4KB (xeno); NbExp=2; IntAct=EBI-2548993, EBI-1053214;
P04049:RAF1 (xeno); NbExp=2; IntAct=EBI-2548993, EBI-365996;
P29353:SHC1 (xeno); NbExp=2; IntAct=EBI-2548993, EBI-78835;
Q92844:TANK (xeno); NbExp=2; IntAct=EBI-2548993, EBI-356349;
P55916:UCP3 (xeno); NbExp=2; IntAct=EBI-2548993, EBI-9116865;
-!- SUBCELLULAR LOCATION: Host nucleus {ECO:0000255|HAMAP-
Rule:MF_04066}. Host cytoplasm {ECO:0000255|HAMAP-Rule:MF_04066}.
Note=In uninfected, transfected cells, NS1 is localized in the
nucleus. Only in virus infected cells, the nuclear export signal
is unveiled, presumably by a viral protein, and a fraction of NS1
is exported in the cytoplasm. {ECO:0000255|HAMAP-Rule:MF_04066}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=NS1;
IsoId=P03495-1; Sequence=Displayed;
Name=NEP; Synonyms=NS2;
IsoId=P69258-1; Sequence=External;
-!- DOMAIN: The dsRNA-binding region is required for suppression of
RNA silencing. {ECO:0000255|HAMAP-Rule:MF_04066}.
-!- PTM: Upon interferon induction, ISGylated via host HERC5; this
results in the impairment of NS1 interaction with RNA targets due
to its inability to form homodimers and to interact with host
EIF2AK2/PKR. {ECO:0000255|HAMAP-Rule:MF_04066}.
-!- SIMILARITY: Belongs to the influenza A viruses NS1 family.
{ECO:0000255|HAMAP-Rule:MF_04066}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; V01102; CAA24288.1; -; Genomic_RNA.
EMBL; DQ508933; ABF21224.1; -; Genomic_RNA.
PIR; A04088; MNIV1A.
PDB; 1AIL; X-ray; 1.90 A; A=1-72.
PDB; 1NS1; NMR; -; A/B=1-73.
PDB; 2KKZ; NMR; -; A=85-215.
PDB; 2RHK; X-ray; 1.95 A; A/B=85-215.
PDB; 3EE8; X-ray; 2.60 A; A/B=84-205.
PDB; 3EE9; X-ray; 2.14 A; A/B=84-205.
PDB; 3KWG; X-ray; 2.21 A; A/B=78-205.
PDB; 3KWI; X-ray; 2.21 A; A/B=78-205.
PDB; 4NW2; X-ray; 1.90 A; B/D=216-230.
PDB; 4O45; X-ray; 1.87 A; B=216-230.
PDBsum; 1AIL; -.
PDBsum; 1NS1; -.
PDBsum; 2KKZ; -.
PDBsum; 2RHK; -.
PDBsum; 3EE8; -.
PDBsum; 3EE9; -.
PDBsum; 3KWG; -.
PDBsum; 3KWI; -.
PDBsum; 4NW2; -.
PDBsum; 4O45; -.
ProteinModelPortal; P03495; -.
SMR; P03495; -.
DIP; DIP-46282N; -.
ELM; P03495; -.
IntAct; P03495; 58.
OrthoDB; VOG090000NT; -.
EvolutionaryTrace; P03495; -.
Proteomes; UP000153055; Genome.
GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
GO; GO:0003725; F:double-stranded RNA binding; TAS:BHF-UCL.
GO; GO:0052038; P:modulation by symbiont of host intracellular transport; IDA:BHF-UCL.
GO; GO:0019056; P:modulation by virus of host transcription; IDA:BHF-UCL.
GO; GO:0052170; P:negative regulation by symbiont of host innate immune response; IDA:BHF-UCL.
GO; GO:0046775; P:suppression by virus of host cytokine production; IDA:BHF-UCL.
GO; GO:0039524; P:suppression by virus of host mRNA processing; IEA:UniProtKB-KW.
GO; GO:0039580; P:suppression by virus of host PKR activity; IEA:UniProtKB-KW.
GO; GO:0039540; P:suppression by virus of host RIG-I activity; IEA:UniProtKB-KW.
GO; GO:0039502; P:suppression by virus of host type I interferon-mediated signaling pathway; IEA:UniProtKB-KW.
HAMAP; MF_04066; INFV_NS1; 1.
InterPro; IPR000256; Flu_NS1.
InterPro; IPR009068; S15_NS1_RNA-bd.
Pfam; PF00600; Flu_NS1; 1.
SUPFAM; SSF47060; SSF47060; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Complete proteome;
Eukaryotic host gene expression shutoff by virus; Host cytoplasm;
Host gene expression shutoff by virus; Host mRNA suppression by virus;
Host nucleus; Host-virus interaction;
Inhibition of host innate immune response by virus;
Inhibition of host interferon signaling pathway by virus;
Inhibition of host PKR by virus;
Inhibition of host pre-mRNA processing by virus;
Inhibition of host RIG-I by virus;
Inhibition of host RLR pathway by virus;
Interferon antiviral system evasion; RNA-binding; Ubl conjugation;
Viral immunoevasion.
CHAIN 1 237 Non-structural protein 1.
/FTId=PRO_0000078952.
REGION 1 73 RNA-binding and homodimerization.
{ECO:0000255|HAMAP-Rule:MF_04066}.
REGION 180 215 CPSF4-binding. {ECO:0000255|HAMAP-
Rule:MF_04066}.
REGION 223 237 PABPN1-binding.
REGION 223 230 PABPN1-binding. {ECO:0000255|HAMAP-
Rule:MF_04066}.
MOTIF 34 38 Nuclear localization signal.
{ECO:0000255|HAMAP-Rule:MF_04066}.
MOTIF 34 38 Nuclear localization signal 1.
MOTIF 137 146 Nuclear export signal.
{ECO:0000255|HAMAP-Rule:MF_04066}.
MOTIF 216 221 Nuclear localization signal 2.
MUTAGEN 7 8 SS->AA: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 7 8 SS->DL: Complete loss of nuclear mRNA
export inhibition.
{ECO:0000269|PubMed:8139028}.
MUTAGEN 19 20 RK->AA,DL: Complete loss of nuclear mRNA
export inhibition.
{ECO:0000269|PubMed:8139028}.
MUTAGEN 31 32 PF->AA: Complete loss of nuclear mRNA
export inhibition.
{ECO:0000269|PubMed:8139028}.
MUTAGEN 35 38 RLRR->ALAA: 75% loss of nuclear mRNA
export inhibition.
{ECO:0000269|PubMed:8139028}.
MUTAGEN 39 40 DQ->AA: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 48 49 ST->DL: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 62 63 KQ->AA: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 62 63 KQ->DL: Complete loss of nuclear mRNA
export inhibition.
{ECO:0000269|PubMed:8139028}.
MUTAGEN 73 74 SD->DL: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 87 88 SR->DL: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 99 100 SR->DL: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 116 117 CI->DL: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 134 136 FSV->AAA,LDL: Complete loss of nuclear
mRNA export inhibition.
{ECO:0000269|PubMed:8139028}.
MUTAGEN 141 141 L->A: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 144 144 L->A: Complete loss of nuclear mRNA
export inhibition.
{ECO:0000269|PubMed:8139028}.
MUTAGEN 146 146 L->A: Complete loss of nuclear mRNA
export inhibition.
{ECO:0000269|PubMed:8139028}.
MUTAGEN 150 151 FT->AA,DL: Complete loss of nuclear mRNA
export inhibition.
{ECO:0000269|PubMed:8139028}.
MUTAGEN 160 161 IS->AA,DL: Complete loss of nuclear mRNA
export inhibition.
{ECO:0000269|PubMed:8139028}.
MUTAGEN 175 176 KN->AA: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 186 187 EW->AS: Complete loss of CPSF4 binding.
{ECO:0000269|PubMed:11421366}.
MUTAGEN 199 200 QR->AA: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 201 203 FAW->AAA: No effect on CPSF4 binding.
{ECO:0000269|PubMed:11421366}.
MUTAGEN 205 206 SS->AA: No effect on nuclear mRNA export
inhibition. {ECO:0000269|PubMed:8139028}.
MUTAGEN 212 213 PP->AA: No effect on CPSF4 binding.
{ECO:0000269|PubMed:11421366}.
MUTAGEN 219 221 KRK->ARA: No effect on nuclear mRNA
export inhibition.
{ECO:0000269|PubMed:8139028}.
HELIX 3 24 {ECO:0000244|PDB:1AIL}.
HELIX 30 50 {ECO:0000244|PDB:1AIL}.
HELIX 54 69 {ECO:0000244|PDB:1AIL}.
STRAND 88 91 {ECO:0000244|PDB:2RHK}.
HELIX 95 99 {ECO:0000244|PDB:2RHK}.
STRAND 105 112 {ECO:0000244|PDB:2RHK}.
STRAND 115 120 {ECO:0000244|PDB:2RHK}.
STRAND 127 137 {ECO:0000244|PDB:2RHK}.
STRAND 140 151 {ECO:0000244|PDB:2RHK}.
STRAND 156 162 {ECO:0000244|PDB:2RHK}.
STRAND 164 166 {ECO:0000244|PDB:3KWI}.
HELIX 171 187 {ECO:0000244|PDB:2RHK}.
STRAND 191 194 {ECO:0000244|PDB:2RHK}.
HELIX 196 201 {ECO:0000244|PDB:2RHK}.
TURN 202 205 {ECO:0000244|PDB:2KKZ}.
SEQUENCE 237 AA; 26846 MW; 14D0308795627E5E CRC64;
MDSNTVSSFQ VDCFLWHVRK QVVDQELGDA PFLDRLRRDQ KSLRGRGSTL GLNIEAATHV
GKQIVEKILK EESDEALKMT MASTPASRYI TDMTIEELSR DWFMLMPKQK VEGPLCIRID
QAIMDKNIML KANFSVIFDR LETLILLRAF TEEGAIVGEI SPLPSFPGHT IEDVKNAIGV
LIGGLEWNDN TVRVSKTLQR FAWGSSNENG RPPLTPKQKR KMARTARSKV RRDKMAD


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