P03496 (NS1_I34A1) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Non-structural protein 1
Short name=NS1

Alternative name(s):
NS1A

Gene names

Name:

NS

Organism

Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) [Reference proteome]

Taxonomic identifier

211044 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA negative-strand viruses › Orthomyxoviridae › Influenzavirus A › Influenza A virus › H1N1 subtype

Virus host

Aves [TaxID: 8782]
Homo sapiens (Human) [TaxID: 9606]
Sus scrofa (Pig) [TaxID: 9823]

Protein attributes

Sequence length	230 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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). This results in the accumulation of unprocessed 3' end pre-mRNAs which can't be exported from the nucleus. 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 By similarity. 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 like 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. Suppresses the RNA silencing-based antiviral response in Drosophila cells By similarity.
Subunit structure	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 By similarity. Ref.6
Subcellular location	Host nucleus. Host cytoplasm. 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 By similarity.
Domain	The dsRNA-binding region is required for suppression of RNA silencing By similarity.
Post-translational modification	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. There are two ISGylated forms: one form is ISGylated at Lys-20, Lys-41, Lys-217, and Lys-219, and another one at Lys-108, Lys-110, and Lys-126, they represent band I and II respectively. Lys-126 and Lys-217 are critical for host antiviral response in vivo. Ref.7
Sequence similarities	Belongs to the influenza A viruses NS1 family.

Ontologies

Keywords
Biological process	Host gene expression shutoff by virus Host mRNA suppression by virus Host-virus interaction Inhibition of host IFN-mediated response initiation by virus Inhibition of host PKR by virus Inhibition of host RIG-I by virus Inhibition of host innate immune response by virus Inhibition of host interferon signaling pathway by virus Inhibition of host pre-mRNA processing by virus Interferon antiviral system evasion Viral immunoevasion
Cellular component	Host cytoplasm Host nucleus
Coding sequence diversity	Alternative splicing
Ligand	RNA-binding
Molecular function	Suppressor of RNA silencing
PTM	Isopeptide bond Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cytokine-mediated signaling pathway Traceable author statement. Source: Reactome evasion or tolerance by virus of host immune response Traceable author statement. Source: Reactome modification by virus of host mRNA processing Traceable author statement. Source: Reactome suppression by virus of host PKR activity Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host RIG-I activity Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host type I interferon production Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host type I interferon-mediated signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW viral transcription Traceable author statement. Source: Reactome
Cellular_component	cytosol Traceable author statement. Source: Reactome host cell cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell nucleoplasm Traceable author statement. Source: Reactome
Molecular_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
TRIM25	Q14258	3	EBI-2547442,EBI-2341129	From a different organism.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform NS1 (identifier: P03496-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform NEP (identifier: P03508-1)

Also known as: NS2;

The sequence of this isoform can be found in the external entry P03508.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 230

230

Non-structural protein 1

PRO_0000078945

Regions

Region

1 – 73

73

RNA-binding and homodimerization By similarity

Region

180 – 215

36

CPSF4-binding By similarity

Region

223 – 230

8

PABPN1-binding By similarity

Motif

34 – 38

5

Nuclear localization signal 1 By similarity

Motif

137 – 146

10

Nuclear export signal By similarity

Motif

216 – 221

6

Nuclear localization signal 2 By similarity

Amino acid modifications

Cross-link

20

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15); in band I form; by host Ref.7

Cross-link

41

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15); in band I form; by host Ref.7

Cross-link

108

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15); in band II form; by host Ref.7

Cross-link

110

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15); in band II form; by host Ref.7

Cross-link

126

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15); in band II form; by host Ref.7

Cross-link

217

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15); in band I form; by host Ref.7

Cross-link

219

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15); in band I form; by host Ref.7

Experimental info

Mutagenesis

20

1

K → A: No of ISGylation of band I form; when associated with K-41; K-217 and K-219. Ref.7

Mutagenesis

38

1

R → A: Complete loss of inhibition of DDX58 CARD ubiquitination; when associated with A-41. Ref.6

Mutagenesis

41

1

K → A: Complete loss of inhibition of DDX58 CARD ubiquitination; when associated with A-38. Ref.6 Ref.7

Mutagenesis

41

1

K → A: No of ISGylation of band I form; when associated with K-20; K-217 and K-219. Ref.6 Ref.7

Mutagenesis

96

1

E → A: Complete loss of inhibition of DDX58 CARD ubiquitination; when associated with A-97. Ref.6

Mutagenesis

97

1

E → A: Complete loss of inhibition of DDX58 CARD ubiquitination; when associated with A-96. Ref.6

Mutagenesis

108

1

K → A: No of ISGylation of band II form; when associated with K-110 and K-126. Ref.7

Mutagenesis

110

1

K → A: No of ISGylation of band II form; when associated with K-108 and K-126. Ref.7

Mutagenesis

126

1

K → A: No of ISGylation of band II form; when associated with K-108 and K-110. Ref.7

Mutagenesis

217

1

K → A: No of ISGylation of band I form; when associated with K-20; K-41 and K-219. Ref.7

Mutagenesis

219

1

K → A: No of ISGylation of band I form; when associated with K-20; K-41 and K-217. Ref.7

Sequence conflict

55

1

E → K in ABD77680. Ref.4

Sequence conflict

101

1

D → E in AAA43536. Ref.2

Secondary structure

1

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230

Helix Strand Turn

Details...

Helix

3 – 24

22

Helix

30 – 50

21

Helix

54 – 69

16

Beta strand

88 – 93

6

Helix

95 – 99

5

Beta strand

105 – 112

8

Beta strand

115 – 120

6

Beta strand

127 – 137

11

Beta strand

140 – 151

12

Beta strand

156 – 162

7

Helix

171 – 187

17

Beta strand

191 – 194

4

Helix

196 – 201

6

Sequences

	Sequence		Length	Mass (Da)
	Isoform NS1 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 2F7EC18E3EE7A4BE	FASTA	230	25,868
	10 20 30 40 50 60 MDPNTVSSFQ VDCFLWHVRK RVADQELGDA PFLDRLRRDQ KSLRGRGSTL GLDIETATRA 70 80 90 100 110 120 GKQIVERILK EESDEALKMT MASVPASRYL TDMTLEEMSR DWSMLIPKQK VAGPLCIRMD 130 140 150 160 170 180 QAIMDKNIIL KANFSVIFDR LETLILLRAF TEEGAIVGEI SPLPSLPGHT AEDVKNAVGV 190 200 210 220 230 LIGGLEWNDN TVRVSETLQR FAWRSSNENG RPPLTPKQKR EMAGTIRSEV
	Isoform NEP (NS2) [UniParc]. See P03508.		–	–

References

[1]	"Complete nucleotide sequence of the influenza A/PR/8/34 virus NS gene and comparison with the NS genes of the A/Udorn/72 and A/FPV/Rostock/34 strains." Baez M., Taussig R., Zazra J.J., Young J.F., Palese P., Reisfeld A., Skalka A.M. Nucleic Acids Res. 8:5845-5858(1980) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Plasmid-only rescue of influenza A virus vaccine candidates." Schickli J.H., Flandorfer A., Nakaya T., Martinez-Sobrido L., Garcia-Sastre A., Palese P. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 356:1965-1973(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[3]	"Efficient generation and growth of influenza virus A/PR/8/34 from eight cDNA fragments." de Wit E., Spronken M.I.J., Bestebroer T.M., Rimmelzwaan G.F., Osterhaus A.D.M.E., Fouchier R.A.M. Virus Res. 103:155-161(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA], REVERSE GENETICS.
[4]	"The NIAID influenza genome sequencing project." Ghedin E., Spiro D., Miller N., Zaborsky J., Feldblyum T., Subbu V., Shumway M., Sparenborg J., Groveman L., Halpin R., Sitz J., Koo H., Salzberg S.L., Webster R.G., Hoffmann E., Krauss S., Naeve C., Bao Y. , Bolotov P., Dernovoy D., Kiryutin B., Lipman D.J., Tatusova T. Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[5]	"Intracellular warfare between human influenza viruses and human cells: the roles of the viral NS1 protein." Krug R.M., Yuan W., Noah D.L., Latham A.G. Virology 309:181-189(2003) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
[6]	"Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I." Gack M.U., Albrecht R.A., Urano T., Inn K.-S., Huang I.-C., Carnero E., Farzan M., Inoue S., Jung J.U., Garcia-Sastre A. Cell Host Microbe 5:439-449(2009) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH HUMAN TRIM25, MUTAGENESIS OF ARG-38; LYS-41; GLU-96 AND GLU-97.
[7]	"Herc5 attenuates influenza A virus by catalyzing ISGylation of viral NS1 protein." Tang Y., Zhong G., Zhu L., Liu X., Shan Y., Feng H., Bu Z., Chen H., Wang C. J. Immunol. 184:5777-5790(2010) [PubMed] [Europe PMC] [Abstract] Cited for: ISGYLATION AT LYS-20; LYS-41; LYS-108; LYS-110; LYS-126; LYS-217 AND LYS-219, MUTAGENESIS OF LYS-20; LYS-41; LYS-108; LYS-110; LYS-126; LYS-217 AND LYS-219.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

V01104 Genomic RNA. Translation: CAA24292.1. Sequence problems.
J02150 Genomic RNA. Translation: AAA43536.1.
AF389122 Genomic RNA. Translation: AAM75163.1.
EF467817 Genomic RNA. Translation: ABO21703.1.
CY009448 Genomic RNA. Translation: ABD77680.1.

RefSeq

NP_040984.1. NC_002020.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2GX9	X-ray	2.10	A/B	79-207	[»]
2ZKO	X-ray	1.70	A/B	1-70	[»]
3L4Q	X-ray	2.30	A/B	73-230	[»]
3O9Q	X-ray	2.50	A/B	79-230	[»]
3O9R	X-ray	2.00	A/B	79-230	[»]
3O9S	X-ray	2.48	A/B	79-230	[»]
3O9T	X-ray	2.20	A/B	79-230	[»]
3O9U	X-ray	3.20	A/B/C/D/E/F/G/H	79-230	[»]
3RVC	X-ray	1.80	A	79-230	[»]

ProteinModelPortal

P03496.

SMR

P03496. Positions 1-72, 79-205.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-29081N.

IntAct

P03496. 172 interactions.

MINT

MINT-3381930.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

956533.

Enzyme and pathway databases

Reactome

REACT_116125. Disease.
REACT_6900. Immune System.

Family and domain databases

Gene3D

1.10.287.10. 1 hit.

InterPro

IPR000256. Flu_NS1.
IPR009068. S15_NS1_RNA-bd.
[Graphical view]

Pfam

PF00600. Flu_NS1. 1 hit.
[Graphical view]

SUPFAM

SSF47060. S15/NS1_bind. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P03496.

Entry information

Entry name

NS1_I34A1

Accession

Primary (citable) accession number: P03496
Secondary accession number(s): Q20N32, Q67267, Q71QT3

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	April 3, 2013
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program