2ic9

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The Coiled-coil Domain (residues 1-93) Structure of the Sin Nombre Virus Nucleocapsid ProteinThe Coiled-coil Domain (residues 1-93) Structure of the Sin Nombre Virus Nucleocapsid Protein

Structural highlights

2ic9 is a 2 chain structure with sequence from Sin Nombre orthohantavirus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NCAP_SINV Encapsidates the genome protecting it from nucleases (Probable). The encapsidated genomic RNA is termed the nucleocapsid (NC) and serves as template for transcription and replication (Probable). The nucleocapsid has a left-handed helical structure (By similarity). As a trimer, specifically binds and acts as a chaperone to unwind the panhandle structure formed by the viral RNA (vRNA) termini (PubMed:15650206, PubMed:15254200, PubMed:21378500, PubMed:16971445, PubMed:25062117, PubMed:16775315). Involved in the transcription and replication initiation of vRNA by mediating primer annealing (PubMed:20164193). Plays a role in cap snatching by sequestering capped RNAs in P bodies for use by the viral RdRp during transcription initiation (PubMed:19047634). Substitutes for the cellular cap-binding complex (eIF4F) to preferentially facilitate the translation of capped mRNAs (PubMed:18971945, PubMed:25062117). Initiates the translation by specifically binding to the cap and 40S ribosomal subunit (PubMed:20844026, PubMed:20164193, PubMed:25062117). Prevents the viral glycoprotein N (Gn) from autophagy-dependent breakdown maybe by blocking autophagosome formation (By similarity). Inhibits host EIF2AK2/PKR dimerization to prevent PKR-induced translational shutdown in cells and thus the activation of the antiviral state (By similarity). Also displays sequence-unspecific DNA endonuclease activity (PubMed:27261891).[UniProtKB:O36307][UniProtKB:P05133][1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Hantaviruses can cause hemorrhagic fever with a renal syndrome and hantavirus pulmonary syndrome when transmitted to humans. The nucleocapsid protein of hantaviruses encapsidates viral genomic RNA and associates with transcription and replication complexes. Both the amino and carboxy termini of the nucleocapsid protein had been predicted to form trimers prior to the formation of the ribonucleoprotein. Crystal structures of amino-terminal fragments of the nucleocapsid protein showed the formation of intramolecular antiparallel coiled coils, but not intermolecular trimers. Thus, the amino-terminal part of the nucleocapsid protein is probably insufficient to initiate the trimerization of the full-length molecule.

The coiled-coil domain structure of the Sin Nombre virus nucleocapsid protein.,Boudko SP, Kuhn RJ, Rossmann MG J Mol Biol. 2007 Mar 9;366(5):1538-44. Epub 2006 Dec 23. PMID:17222867[12]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Mir MA, Panganiban AT. Trimeric hantavirus nucleocapsid protein binds specifically to the viral RNA panhandle. J Virol. 2004 Aug;78(15):8281-8. PMID:15254200 doi:10.1128/JVI.78.15.8281-8288.2004
  2. ↑ Mir MA, Panganiban AT. The hantavirus nucleocapsid protein recognizes specific features of the viral RNA panhandle and is altered in conformation upon RNA binding. J Virol. 2005 Feb;79(3):1824-35. PMID:15650206 doi:10.1128/JVI.79.3.1824-1835.2005
  3. ↑ Mir MA, Panganiban AT. Characterization of the RNA chaperone activity of hantavirus nucleocapsid protein. J Virol. 2006 Jul;80(13):6276-85. PMID:16775315 doi:10.1128/JVI.00147-06
  4. ↑ Mir MA, Brown B, Hjelle B, Duran WA, Panganiban AT. Hantavirus N protein exhibits genus-specific recognition of the viral RNA panhandle. J Virol. 2006 Nov;80(22):11283-92. PMID:16971445 doi:10.1128/JVI.00820-06
  5. ↑ Mir MA, Panganiban AT. A protein that replaces the entire cellular eIF4F complex. EMBO J. 2008 Dec 3;27(23):3129-39. PMID:18971945 doi:10.1038/emboj.2008.228
  6. ↑ Mir MA, Duran WA, Hjelle BL, Ye C, Panganiban AT. Storage of cellular 5' mRNA caps in P bodies for viral cap-snatching. Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19294-9. PMID:19047634 doi:10.1073/pnas.0807211105
  7. ↑ Mir MA, Sheema S, Haseeb A, Haque A. Hantavirus nucleocapsid protein has distinct m7G cap J Biol Chem. 2010 Apr 9;285(15):11357-68. PMID:20164193 doi:10.1074/jbc.M110.102459
  8. ↑ Haque A, Mir MA. Interaction of hantavirus nucleocapsid protein with ribosomal protein S19. J Virol. 2010 Dec;84(23):12450-3. PMID:20844026 doi:10.1128/JVI.01388-10
  9. ↑ Brown BA, Panganiban AT. Identification of a region of hantavirus nucleocapsid protein required for RNA chaperone activity. RNA Biol. 2010 Nov-Dec;7(6):830-7. PMID:21378500 doi:10.4161/rna.7.6.13862
  10. ↑ Ganaie SS, Haque A, Cheng E, Bonny TS, Salim NN, Mir MA. Ribosomal protein S19-binding domain provides insights into hantavirus nucleocapsid protein-mediated translation initiation mechanism. Biochem J. 2014 Nov 15;464(1):109-21. PMID:25062117 doi:10.1042/BJ20140449
  11. ↑ Möncke-Buchner E, Szczepek M, Bokelmann M, Heinemann P, Raftery MJ, Krüger DH, Reuter M. Sin Nombre hantavirus nucleocapsid protein exhibits a metal-dependent DNA-specific endonucleolytic activity. Virology. 2016 Sep;496:67-76. PMID:27261891 doi:10.1016/j.virol.2016.05.009
  12. ↑ Boudko SP, Kuhn RJ, Rossmann MG. The coiled-coil domain structure of the Sin Nombre virus nucleocapsid protein. J Mol Biol. 2007 Mar 9;366(5):1538-44. Epub 2006 Dec 23. PMID:17222867 doi:10.1016/j.jmb.2006.12.046

2ic9, resolution 2.00Å

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