Nucleoprotein: Difference between revisions

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[[Image:3pto.png|left|200px|thumb|Crystal Structure of Nucleoprotein [[3pto]]]]
<StructureSection load='' size='350' side='right' caption='Nucleoprotein from Lassa virus trimer complex with TTP and Zn+2 ions (grey) [[3mx2]]' scene='46/461363/Cv/2' pspeed='8'>
{{STRUCTURE_3pto|  PDB=3pto  | SIZE=300| SCENE= |right|CAPTION=Nucleoprotein [[3pto]] }}


'''Nucleoproteins''' (NP) are associated with DNA or RNA.  NPs which contain RNA are called ribonucleoproteins (RNPs).  The NP RNA-recognition motif is named RRM.  The small nuclear ribonucleoproteins (snRNPs) are RNA-protein complexes which form part of the spliceosome.  The heterogenous nuclear ribonucleoproteins (hnRNP) are RNA-protein complexes which associates with the splicing apparatus and prevent the folding of pre-mRNA. The images at the left and at the right correspond to one representative NP, ''i.e.'' the crystal structure of Nucleoprotein from Vesicular stomatitis Indiana virus ([[3pto]]).
__TOC__
== Function ==


{{TOC limit|limit=2}}
'''Nucleoproteins''' (NP) or '''nucleocapsid proteins''' are proteins associated with DNA or RNA<ref>PMID:2203758</ref>.  NPs which contain RNA are called '''ribonucleoproteins''' (RNPs).  The NP RNA-recognition motif is named RRM.<br />
<br />
The '''small nuclear ribonucleoproteins''' (snRNPs) are RNA-protein complexes which form part of the spliceosome<ref>PMID:15130578</ref>.  For details on SnRNP see [[Azoarcus group I intron]].<br />
<br />
The '''heterogenous nuclear ribonucleoproteins''' (hnRNP) are RNA-protein complexes which associates with the splicing apparatus and prevent the folding of pre-mRNA<ref>PMID:19099192</ref>. <br />
<br />
For details on '''heterogenous nuclear ribonucleoproteins''' see [[HnRNP A1]].<br />
<br />
For homology model and multiple sequence alignment see [[User:Michael Strong/H1N1/NP]] and [[User:Michael Strong/H1N1/NP/MSA]].<br />
<br />
For details on HIV-1 nucleoprotein see [[HIV-1 Nucleocapsid Protein (NC)]].
== 3D Structures of Nucleoprotein ==


[[3ouo]], [[3ov9]] – NP – Rift valley fever virus
== Structural highlights ==
[[3q7b]], [[3q7c]], [[3mwp]], [[3mwt]] – LvNP exonuclease domain – Lassa virus
*<scene name='46/461363/Cv/6'>TTP binding site</scene> in Nucleoprotein from Lassa virus ([[3mx2]]). Water molecules are shown as red spheres.
[[3pto]] - VvNP – Vesicular stomatitis Indiana virus
*<scene name='46/461363/Cv/7'>Zn coordination site</scene>.
[[2qvj]] – VvNP (mutant)
[[2k48]] – NP N terminal – Andes virus - NMR
[[3hd4]] – NP N terminal – Murine hepatitis virus
[[2wfs]] – IvNP – Cryo EM – Influenza virus
[[2q06]], [[2iqh]] – IvNP
[[2i8b]] – NP C terminal – Ebola virus – NMR
[[1yvr]] – XlNP Ro – Xenopus laevis
[[1wwf]] – MvNP P10 – Moloney murine leukemia virus – NMR
[[2c86]] – BvNP N terminal – Avian infectious bronchitis virus
[[2ca1]] – BvNP dimerization domain
[[2btl]], [[2bxx]] – BvNP RRM (mutant)
1n93, 1pp1 – NP P40 – Borna disease virus


Nucleoprotein binary complex
== 3D Structures of Nucleoprotein ==
 
[[Nucleoprotein 3D structures]]
3mx2, 3mx5 – LvNP + nucleotide
3ptx, 3pu0, 3pu1, 3pu4, 2gic – VvNP + RNA
2wyy – VvNP + poly U – Cryo EM
3hhw – VvNP + phosphoprotein
3hhz - VvNP + phosphoprotein + RNA
2wj8 – NP + RNA – Human respiratory syncytial virus
2i91, 1yvp – XlNP Ro + RNA
2gtt – NP + RNA – Rabies virus
1wwg, 1wwd, 1wwe , 1u6p- MvNP P10 + RNA – NMR
 
Ribonucleoprotein
 
2lbw – yRNP subunit 2 residues 36-156 (mutant) – yeast – NMR
2lbx - yRNP subunit 2 residues 36-156 – NMR
 
Small nuclear ribonucleoprotein
 
2a3j - h-snRNP U1 A RRM – human - NMR
2l5i, 2l5j - h-snRNP U1 70kDa residues 131-151 – NMR
2vy4, 2vy5 - h-snRNP U11/U12 – NMR
2cqj - h-snRNP U3 S4 domain – NMR
1x4q - h-snRNP U4/U6 PWI domain - NMR
2vrd - h-snRNP U1 C zinc finger domain - NMR
2k3k – Dm-snRNP U1 A RRM1 – Drosophila melanogaster – NMR
2aym - Dm-snRNP U1 A
2b0g - Dm-snRNP U1 A RBD2 – NMR
 
Small nuclear ribonucleoprotein binary complex
 
3plu, 3plv – y-snRNP HINDI domain + ubiquitin-like modifier HUB1
2y9a, 2y9b, 2y9c, 2y9d – h-snRNP  U4 core domain
3p49 - h-snRNP A RRM + glycine riboswitch RNA
3pgw, 3mum, 3mur, 3mut, 3muv, 3egz - h-snRNP U1 A + DNA riboswitch
3mxh, 3irw - h-snRNP U1 A (mutant) + DNA riboswitch
3k0j - h-snRNP U1 A (mutant) + RNA
3iin - h-snRNP U1 A (mutant) + group I intron + DNA
3b02, 3b03, 3b04 - h-snRNP U1 A RRM1 + group I intron + RNA
1zzn - h-snRNP U1 A RRM1 (mutant) + group I intron + RNA
3l3c, 3g8s, 3g8t, 3g96, 3g9c, 2nz4 - h-snRNP U1 A (mutant) + GLMS ribozyme + RNA
3hhn - h-snRNP U1 A (mutant) + class I ligase ribozyme
2oih, 2oj3 - h-snRNP U1 A + HDV ribozyme
3cul, 3cun - h-snRNP U1 A (mutant) + aminoacyl-tRNA synthetase ribozyme
3cw1 - h-snRNP U1 in spliceosome
2ozb - h-snRNP U4/U6 + NHP2-like protein + RNA
2bn5 - Dm-snRNP U1 70kDa + PSI B box – NMR
 
Heterogenous nuclear ribonucleoprotein
 
3s01 – m-hnRNP L RRM3 domain – mouse
2e5i - m-hnRNP L RRM – NMR
2db1 - m-hnRNP F RRM – NMR
1x4b - h-hnRNP A2/B1 RRM – NMR
1txp - h-hnRNP C oligomerization domain – NMR
1wf2 - h-hnRNP C1/C2 RRM – NMR
2hgl, 2hgm, 2hgn - h-hnRNP F QRRM – NMR
1wg5, 1wez - h-hnRNP H RRM – NMR
2ad9, 2adb, 2adc - h-hnRNP I – NMR
1zzi, 1zzj - h-hnRNP K KH domain + DNA
1zzk - h-hnRNP K KH domain
2do0, 2dh9, 2dgv - h-hnRNP M RRM – NMR
2dgu - h-hnRNP Q RRM – NMR
2dk2 - h-hnRNP R RRM – NMR


Heterogenous nuclear ribonucleoprotein binary complex
</StructureSection>


2kfy, 2kg0, 2kg1 - h-hnRNP F QRRM + DNA – NMR
== References ==
2z5n, 2z5o, 2ot8 - h-hnRNP D0 C terminal + transportin-1
<references/>
1u1k, 1u1l, 1u1m, 1u1n, 1u1o, 1u1p, 1u1q, 1u1r - h-hnRNP A1 + DNA
[[Category:Topic Page]]
1wtb, 1x0f - h-hnRNP D0 RRM + DNA – NMR
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