PDBsum entry 1pd3

Unknown function

PDB id

1pd3

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Contents

			Protein chains

					54 a.a.

PDB id:

1pd3

Links

Name:

Unknown function

Title:

Influenza a nep m1-binding domain

Structure:

Nonstructural protein ns2. Chain: a, b. Fragment: residues 59-116. Engineered: yes. Other_details: m1-binding domain of nep

Source:

Influenza a virus. Organism_taxid: 11320. Gene: ns2. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.60Å

R-factor:

0.179

R-free:

0.244

Authors:

F.Baudin

Key ref:

H.Akarsu et al. (2003). Crystal structure of the M1 protein-binding domain of the influenza A virus nuclear export protein (NEP/NS2). Embo J, 22, 4646-4655. PubMed id: 12970177

Date:

19-May-03

Release date:

16-Dec-03

PROCHECK

	Headers

	References

Protein chains

P03508 (NEP_I34A1) - Nuclear export protein from Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)

Seq: Struc:					121 a.a. 54 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.?

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	Embo J 22:4646-4655 (2003)
PubMed id: 12970177

Crystal structure of the M1 protein-binding domain of the influenza A virus nuclear export protein (NEP/NS2).
H.Akarsu, W.P.Burmeister, C.Petosa, I.Petit, C.W.Müller, R.W.Ruigrok, F.Baudin.

ABSTRACT

During influenza virus infection, viral ribonucleoproteins (vRNPs) are replicated in the nucleus and must be exported to the cytoplasm before assembling into mature viral particles. Nuclear export is mediated by the cellular protein Crm1 and putatively by the viral protein NEP/NS2. Proteolytic cleavage of NEP defines an N-terminal domain which mediates RanGTP-dependent binding to Crm1 and a C-terminal domain which binds to the viral matrix protein M1. The 2.6 A crystal structure of the C-terminal domain reveals an amphipathic helical hairpin which dimerizes as a four-helix bundle. The NEP-M1 interaction involves two critical epitopes: an exposed tryptophan (Trp78) surrounded by a cluster of glutamate residues on NEP, and the basic nuclear localization signal (NLS) of M1. Implications for vRNP export are discussed.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21338659

O.V.Chervyakova, V.M.Strochkov, K.T.Sultankulova, N.T.Sandybayev, V.L.Zaitsev, and S.M.Mamadaliyev (2011).
Molecular and genetic analysis of NS gene from high pathogenic strains of the avian influenza (H5N1) virus isolated in Kazakhstan.

Gene, 476, 15-19.

20554795

J.Chen, S.Huang, and Z.Chen (2010).
Human cellular protein nucleoporin hNup98 interacts with influenza A virus NS2/nuclear export protein and overexpression of its GLFG repeat domain can inhibit virus propagation.

J Gen Virol, 91, 2474-2484.

20498070

L.J.Calder, S.Wasilewski, J.A.Berriman, and P.B.Rosenthal (2010).
Structural organization of a filamentous influenza A virus.

Proc Natl Acad Sci U S A, 107, 10685-10690.

20519456

N.C.Robb, D.Jackson, F.T.Vreede, and E.Fodor (2010).
Splicing of influenza A virus NS1 mRNA is independent of the viral NS1 protein.

J Gen Virol, 91, 2331-2340.

20140252

O.Miotto, A.T.Heiny, R.Albrecht, A.García-Sastre, T.W.Tan, J.T.August, and V.Brusic (2010).
Complete-proteome mapping of human influenza A adaptive mutations: implications for human transmissibility of zoonotic strains.

PLoS One, 5, e9025.

20853340

T.Noda, and Y.Kawaoka (2010).
Structure of influenza virus ribonucleoprotein complexes and their packaging into virions.

Rev Med Virol, 20, 380-391.

19481124

D.P.Nayak, R.A.Balogun, H.Yamada, Z.H.Zhou, and S.Barman (2009).
Influenza virus morphogenesis and budding.

Virus Res, 143, 147-161.

19656971

J.Zhang, G.Li, X.Liu, Z.Wang, W.Liu, and X.Ye (2009).
Influenza A virus M1 blocks the classical complement pathway through interacting with C1qA.

J Gen Virol, 90, 2751-2758.

20015386

L.Deng, J.Guan, Q.Dong, and S.Zhou (2009).
Prediction of protein-protein interaction sites using an ensemble method.

BMC Bioinformatics, 10, 426.

19336399

L.Nencioni, G.De Chiara, R.Sgarbanti, D.Amatore, K.Aquilano, M.E.Marcocci, A.Serafino, M.Torcia, F.Cozzolino, M.R.Ciriolo, E.Garaci, and A.T.Palamara (2009).
Bcl-2 expression and p38MAPK activity in cells infected with influenza A virus: impact on virally induced apoptosis and viral replication.

J Biol Chem, 284, 16004-16015.

19264657

N.C.Robb, M.Smith, F.T.Vreede, and E.Fodor (2009).
NS2/NEP protein regulates transcription and replication of the influenza virus RNA genome.

J Gen Virol, 90, 1398-1407.

19297465

R.Ghildyal, A.Ho, M.Dias, L.Soegiyono, P.G.Bardin, K.C.Tran, M.N.Teng, and D.A.Jans (2009).
The respiratory syncytial virus matrix protein possesses a Crm1-mediated nuclear export mechanism.

J Virol, 83, 5353-5362.

18987140

S.L.Noton, M.Simpson-Holley, E.Medcalf, H.M.Wise, E.C.Hutchinson, J.W.McCauley, and P.Digard (2009).
Studies of an influenza A virus temperature-sensitive mutant identify a late role for NP in the formation of infectious virions.

J Virol, 83, 562-571.

19927983

T.Naito, A.Kawaguchi, and K.Nagata (2009).
[Function of influenza virus RNA polymerase based on structure].

Uirusu, 59, 1.

20027280

T.Samji (2009).
Influenza A: understanding the viral life cycle.

Yale J Biol Med, 82, 153-159.

19420157

V.Darapaneni, V.K.Prabhaker, and A.Kukol (2009).
Large-scale analysis of influenza A virus sequences reveals potential drug target sites of non-structural proteins.

J Gen Virol, 90, 2124-2133.

18815312

C.Li, M.Hatta, S.Watanabe, G.Neumann, and Y.Kawaoka (2008).
Compatibility among polymerase subunit proteins is a restricting factor in reassortment between equine H7N7 and human H3N2 influenza viruses.

J Virol, 82, 11880-11888.

19026786

K.D.Swanson, Y.Tang, D.F.Ceccarelli, F.Poy, J.P.Sliwa, B.G.Neel, and M.J.Eck (2008).
The Skap-hom dimerization and PH domains comprise a 3'-phosphoinositide-gated molecular switch.

Mol Cell, 32, 564-575.

PDB codes:

1u5g 2otx

18411420

P.O.Ilyinskii, A.B.Meriin, V.L.Gabai, E.V.Usachev, A.G.Prilipov, G.Thoidis, and A.M.Shneider (2008).
The proteosomal degradation of fusion proteins cannot be predicted from the proteosome susceptibility of their individual components.

Protein Sci, 17, 1077-1085.

19077274

S.Zohari, P.Gyarmati, A.Ejdersund, U.Berglöf, P.Thorén, M.Ehrenberg, G.Czifra, S.Belák, J.Waldenström, B.Olsen, and M.Berg (2008).
Phylogenetic analysis of the non-structural (NS) gene of influenza A viruses isolated from mallards in Northern Europe in 2005.

Virol J, 5, 147.

18172752

S.Zohari, P.Gyarmati, P.Thorén, G.Czifra, C.Bröjer, S.Belák, and M.Berg (2008).
Genetic characterization of the NS gene indicates co-circulation of two sub-lineages of highly pathogenic avian influenza virus of H5N1 subtype in Northern Europe in 2006.

Virus Genes, 36, 117-125.

17652405

D.B.Finkelstein, S.Mukatira, P.K.Mehta, J.C.Obenauer, X.Su, R.G.Webster, and C.W.Naeve (2007).
Persistent host markers in pandemic and H5N1 influenza viruses.

J Virol, 81, 10292-10299.

17622633

S.L.Noton, E.Medcalf, D.Fisher, A.E.Mullin, D.Elton, and P.Digard (2007).
Identification of the domains of the influenza A virus M1 matrix protein required for NP binding, oligomerization and incorporation into virions.

J Gen Virol, 88, 2280-2290.

16474136

E.K.Hui, S.Barman, D.H.Tang, B.France, and D.P.Nayak (2006).
YRKL sequence of influenza virus M1 functions as the L domain motif and interacts with VPS28 and Cdc42.

J Virol, 80, 2291-2308.

16987982

P.K.Singhal, P.Rajendra Kumar, M.R.Subba Rao, and S.Mahalingam (2006).
Nuclear export of simian immunodeficiency virus Vpx protein.

J Virol, 80, 12271-12282.

15661164

I.Garcia-Robles, H.Akarsu, C.W.Müller, R.W.Ruigrok, and F.Baudin (2005).
Interaction of influenza virus proteins with nucleosomes.

Virology, 332, 329-336.

15650216

T.Liu, and Z.Ye (2005).
Attenuating mutations of the matrix gene of influenza A/WSN/33 virus.

J Virol, 79, 1918-1923.

15108720

J.Timmins, R.W.Ruigrok, and W.Weissenhorn (2004).
Structural studies on the Ebola virus matrix protein VP40 indicate that matrix proteins of enveloped RNA viruses are analogues but not homologues.

FEMS Microbiol Lett, 233, 179-186.

15331747

K.Iwatsuki-Horimoto, T.Horimoto, Y.Fujii, and Y.Kawaoka (2004).
Generation of influenza A virus NS2 (NEP) mutants with an altered nuclear export signal sequence.

J Virol, 78, 10149-10155.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.