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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_3mx2| PDB=3mx2 | SIZE=400| SCENE= |right|CAPTION=Nucleoprotein from Lassa virus trimer complex with TTP and Zn+2 ions [[3mx2]] }}
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| '''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]]). For homology model and multiple sequence alignment see [[User:Michael Strong/H1N1/NP]] and [[User:Michael Strong/H1N1/NP/MSA]].
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| | == Function == |
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| == 3D Structures of Nucleoprotein == | |
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| ''Updated February 2013'' | | '''Nucleoproteins''' (NP) 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 /> |
| | 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 /> |
| | 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 /> |
| | For details on '''heterogenous nuclear ribonucleoproteins''' see [[HnRNP A1]].<br /> |
| | For homology model and multiple sequence alignment see [[User:Michael Strong/H1N1/NP]] and [[User:Michael Strong/H1N1/NP/MSA]].<br /> |
| | For details on HIV-1 nucleoprotein see [[HIV-1 Nucleocapsid Protein (NC)]]. |
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| ===Nucleoprotein=== | | == Structural highlights == |
| | *<scene name='46/461363/Cv/6'>TTP binding site</scene> in Nucleoprotein from Lassa virus ([[3mx2]]). Water molecules are shown as red spheres. |
| | *<scene name='46/461363/Cv/7'>Zn coordination site</scene>. |
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| [[3ouo]], [[3ov9]] – NP – Rift valley fever virus<br />
| | == 3D Structures of Nucleoprotein == |
| [[3q7b]], [[3q7c]] – LvNP exonuclease domain – Lassa virus<br />
| | [[Nucleoprotein 3D structures]] |
| [[3mwp]], [[3mwt]], [[3r3l]] – LvNP<br />
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| [[3pto]] - VvNP – Vesicular stomatitis Indiana virus<br />
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| [[2qvj]] – VvNP (mutant)<br />
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| [[2k48]] – NP N terminal – Andes virus - NMR<br />
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| [[1ssk]] - ScvNP N terminal – SARS coronavirus – NMR<br />
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| [[2gib]] – ScvNP dimerization domain<br />
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| [[2jw8]] - ScvNP dimerization domain – NMR<br />
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| [[2ofz]], [[2og3]] - ScvNP RNA-binding domain<br />
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| [[3hd4]] – NP N terminal – Murine hepatitis virus<br />
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| [[2wfs]], [[2ymn]] – IvNP – Cryo EM – Influenza virus<br />
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| [[2q06]], [[2iqh]], [[3tj0]] – IvNP<br />
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| [[2i8b]] – EvNP C terminal – Ebola virus – NMR<br />
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| [[3v7o]] - EvNP C terminal<br />
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| [[1yvr]] – XlNP Ro – ''Xenopus laevis''<br />
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| [[1wwf]] – MvNP P10 – Moloney murine leukemia virus – NMR<br />
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| [[2c86]], [[2gec]] – BvNP N terminal – Avian infectious bronchitis virus<br />
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| [[2ca1]], [[2ge7]], [[2ge8]] – BvNP dimerization domain<br />
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| [[2btl]], [[2bxx]] – BvNP RRM (mutant)<br />
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| [[1n93]], [[1pp1]] – NP P40 – Borna disease virus<br />
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| [[4aqf]], [[4aqg]] – NP N – Crimean-Congo hemorrhagic fever virus<br />
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| [[4fi5]] – NP N terminal – Hantaan virus<br />
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| [[4h5l]] – NP – Toscana virus
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| ===Nucleoprotein binary complex===
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| [[3mx2]], [[3mx5]] – LvNP + nucleotide<br /> | |
| [[3t5n]], [[3t5q]], [[4fvu]] – LvNP + RNA<br />
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| [[3ptx]], [[3pu0]], [[3pu1]], [[3pu4]], [[2gic]] – VvNP + RNA<br />
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| [[2wyy]] – VvNP + poly U – Cryo EM<br />
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| [[3hhw]], [[3pmk]] – VvNP + phosphoprotein<br />
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| [[3hhz]] - VvNP + phosphoprotein + RNA<br />
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| [[2wj8]], [[2yhm]] – NP + RNA – Human respiratory syncytial virus<br />
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| [[2i91]], [[1yvp]] – XlNP Ro + RNA <br />
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| [[2gtt]] – NP + RNA – Rabies virus<br />
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| [[1wwg]], [[1wwd]], [[1wwe]], [[1u6p]] - MvNP P10 + RNA – NMR<br />
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| [[3ro5]] – IvNP + ligand<br />
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| [[4bbl]] – IvNP + RNA – Cryo EM
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| ===Ribonucleoprotein===
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| [[2lbw]] – yRNP subunit 2 residues 36-156 (mutant) – yeast – NMR<br />
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| [[2lbx]] - yRNP subunit 2 residues 36-156 – NMR<br />
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| ===Small nuclear ribonucleoprotein===
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| [[2a3j]], [[1fht]] - h-snRNP U1 A RRM – human - NMR<br />
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| [[2u1a]] - h-snRNP U1 A RRM (mutant) – NMR<br />
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| [[1oia]] - h-snRNP U1 A RRM<br />
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| [[2l5i]], [[2l5j]] - h-snRNP U1 70kDa residues 131-151 – NMR<br />
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| [[2vy4]], [[2vy5]] - h-snRNP U11/U12 – NMR<br />
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| [[2cqj]] - h-snRNP U3 S4 domain – NMR<br />
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| [[1x4q]] - h-snRNP U4/U6 PWI domain - NMR<br />
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| [[2vrd]] - h-snRNP U1 C zinc finger domain - NMR<br />
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| [[1b34]] - h-snRNP D1 + h-snRNP D2<br />
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| [[2k3k]] – Dm-snRNP U1 A RRM1 – ''Drosophila melanogaster'' – NMR<br />
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| [[2aym]] - Dm-snRNP U1 A<br />
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| [[2b0g]] - Dm-snRNP U1 A RBD2 – NMR<br />
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| [[1n9r]], [[1n9s]] – y-snRNP F
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| ===Small nuclear ribonucleoprotein binary complex===
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| [[3plu]], [[3plv]] – y-snRNP HINDI domain + ubiquitin-like modifier HUB1<br />
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| [[2y9a]], [[2y9b]], [[2y9c]], [[2y9d]] – h-snRNP U4 core domain<br />
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| [[3p49]] - h-snRNP A RRM + glycine riboswitch RNA<br />
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| [[3iwn]] - h-snRNP U1 A RRM (mutant) + riboswitch RNA<br />
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| [[3pgw]], [[3mum]], [[3mur]], [[3mut]], [[3muv]], [[3egz]] - h-snRNP U1 A + DNA riboswitch<br />
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| [[3mxh]], [[3irw]] - h-snRNP U1 A (mutant) + DNA riboswitch<br />
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| [[3k0j]], [[1drz]], [[1m5k]], [[1m5o]], [[1m5p]], [[1m5v]], [[1u6b]] - h-snRNP U1 A (mutant) + RNA<br />
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| [[3bo2]], [[3bo3]], [[3bo4]] - h-snRNP U1 A RRM + RNA<br />
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| [[1sj3]], [[1sj4]], [[1sjf]], [[1vbx]], [[1vby]], [[1vbz]], [[1vc0]], [[1vc5]], [[1vc6]], [[1vc7]] - h-snRNP U1 A (mutant) + Hepatitis ribozyme<br />
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| [[3r1h]], [[3r1l]] - h-snRNP U1 A (mutant) + ribozyme<br />
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| [[1aud]] - h-snRNP U1 A (mutant) + RNA - NMR<br />
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| [[3iin]] - h-snRNP U1 A (mutant) + group I intron + DNA<br />
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| [[3b02]], [[3b03]], [[3b04]] - h-snRNP U1 A RRM1 + group I intron + RNA<br />
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| [[1zzn]] - h-snRNP U1 A RRM1 (mutant) + group I intron + RNA<br />
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| [[3l3c]], [[3g8s]], [[3g8t]], [[3g96]], [[3g9c]], [[2nz4]] - h-snRNP U1 A (mutant) + GLMS ribozyme + RNA<br />
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| [[3hhn]] - h-snRNP U1 A (mutant) + class I ligase ribozyme<br />
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| [[2oih]], [[2oj3]] - h-snRNP U1 A + HDV ribozyme<br />
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| [[3cul]], [[3cun]] - h-snRNP U1 A (mutant) + aminoacyl-tRNA synthetase ribozyme<br />
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| [[3cw1]] - h-snRNP U1 in spliceosome<br />
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| [[2ozb]], [[3siu]], [[3siv]] - h-snRNP U4/U6 + NHP2-like protein + RNA<br />
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| [[3s6n]] - h-snRNP D1 + h-snRNP D2 + h-snRNP E + h-snRNP F + h-snRNP G + survival motor neuron protein + SMN interacting protein<br />
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| [[2bn5]] - Dm-snRNP U1 70kDa + PSI B box – NMR<br />
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| ===Heterogenous nuclear ribonucleoprotein===
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| [[3s01]] – m-hnRNP L RRM3 domain – mouse<br />
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| [[3tyt]] - m-hnRNP L<br />
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| [[2e5i]] - m-hnRNP L RRM – NMR<br />
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| [[2db1]] - m-hnRNP F RRM – NMR<br />
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| [[1ha1]], [[1l3k]], [[1up1]] - h-hnRNP A1 RRM<br />
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| [[3s7r]] - h-hnRNP A/B<br />
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| [[1x4b]] - h-hnRNP A2/B1 RRM – NMR<br />
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| [[1txp]] - h-hnRNP C oligomerization domain – NMR<br />
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| [[1wf2]] - h-hnRNP C1/C2 RRM – NMR<br />
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| [[1hd0]], [[1hd1]], [[1iqt]] - h-hnRNP D0 RRM – NMR<br />
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| [[2hgl]], [[2hgm]], [[2hgn]] - h-hnRNP F QRRM – NMR<br />
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| [[1wg5]], [[1wez]] - h-hnRNP H RRM – NMR<br />
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| [[2ad9]], [[2adb]], [[2adc]] - h-hnRNP I – NMR<br />
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| [[1zzk]] - h-hnRNP K KH domain<br />
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| [[3r27]], [[3t08]] - h-hnRNP L RRM<br />
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| [[2do0]], [[2dh9]], [[2dgv]] - h-hnRNP M RRM – NMR<br />
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| [[2dgu]] - h-hnRNP Q RRM – NMR<br />
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| [[2dk2]] - h-hnRNP R RRM – NMR<br />
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| ===Heterogenous nuclear ribonucleoprotein binary complex===
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| [[2kfy]], [[2kg0]], [[2kg1]] - h-hnRNP F QRRM + DNA – NMR<br />
| | </StructureSection> |
| [[2z5n]], [[2z5o]], [[2ot8]] - h-hnRNP D0 CTD + transportin-1<br />
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| [[1u1k]], [[1u1l]], [[1u1m]], [[1u1n]], [[1u1o]], [[1u1p]], [[1u1q]], [[1u1r]], [[1up1]] - h-hnRNP A1 RRM + DNA<br />
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| [[1pgz]], [[1po6]] - h-hnRNP A1 + DNA + inhibitor<br />
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| [[1wtb]], [[1x0f]] - h-hnRNP D0 RRM + DNA – NMR<br />
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| [[1zzi]], [[1zzj]] - h-hnRNP K KH domain + DNA<br />
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| [[1j5k]] - h-hnRNP K KH domain + DNA – NMR
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| | == References == |
| | <references/> |
| [[Category:Topic Page]] | | [[Category:Topic Page]] |