Nucleoprotein

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:15, 9 January 2020) (edit) (undo)
 
(27 intermediate revisions not shown.)
Line 1: Line 1:
-
[[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]] }}
+
 +
__TOC__
 +
== Function ==
 +
'''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)]].
 +
== 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>.
- 
- 
- 
- 
- 
- 
- 
- 
- 
- 
- 
- 
- 
- 
- 
- 
- 
-
'''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]].
 
-
{{TOC limit|limit=2}}
 
-
<br />
 
-
<br />
 
-
<br />
 
-
<br />
 
-
<br />
 
== 3D Structures of Nucleoprotein ==
== 3D Structures of Nucleoprotein ==
 +
[[Nucleoprotein 3D structures]]
-
''Updated February 2013''
+
</StructureSection>
-
 
+
-
===Nucleoprotein===
+
-
 
+
-
[[3ouo]], [[3ov9]] – NP – Rift valley fever virus<br />
+
-
[[3q7b]], [[3q7c]] – LvNP exonuclease domain – Lassa virus<br />
+
-
[[3mwp]], [[3mwt]], [[3r3l]] – LvNP<br />
+
-
[[3pto]] - VvNP – Vesicular stomatitis Indiana virus<br />
+
-
[[2qvj]] – VvNP (mutant)<br />
+
-
[[2k48]] – NP N terminal – Andes virus - NMR<br />
+
-
[[1ssk]] - ScvNP N terminal – SARS coronavirus – NMR<br />
+
-
[[2gib]] – ScvNP dimerization domain<br />
+
-
[[2jw8]] - ScvNP dimerization domain – NMR<br />
+
-
[[2ofz]], [[2og3]] - ScvNP RNA-binding domain<br />
+
-
[[3hd4]] – NP N terminal – Murine hepatitis virus<br />
+
-
[[2wfs]], [[2ymn]] – IvNP – Cryo EM – Influenza virus<br />
+
-
[[2q06]], [[2iqh]], [[3tj0]] – IvNP<br />
+
-
[[2i8b]] – EvNP C terminal – Ebola virus – NMR<br />
+
-
[[3v7o]] - EvNP C terminal<br />
+
-
[[1yvr]] – XlNP Ro – ''Xenopus laevis''<br />
+
-
[[1wwf]] – MvNP P10 – Moloney murine leukemia virus – NMR<br />
+
-
[[2c86]], [[2gec]] – BvNP N terminal – Avian infectious bronchitis virus<br />
+
-
[[2ca1]], [[2ge7]], [[2ge8]] – BvNP dimerization domain<br />
+
-
[[2btl]], [[2bxx]] – BvNP RRM (mutant)<br />
+
-
[[1n93]], [[1pp1]] – NP P40 – Borna disease virus<br />
+
-
[[4aqf]], [[4aqg]] – NP N – Crimean-Congo hemorrhagic fever virus<br />
+
-
[[4fi5]] – NP N terminal – Hantaan virus<br />
+
-
[[4h5l]] – NP – Toscana virus
+
-
 
+
-
===Nucleoprotein binary complex===
+
-
 
+
-
[[3mx2]], [[3mx5]] – LvNP + nucleotide<br />
+
-
[[3t5n]], [[3t5q]], [[4fvu]] – LvNP + RNA<br />
+
-
[[3ptx]], [[3pu0]], [[3pu1]], [[3pu4]], [[2gic]] – VvNP + RNA<br />
+
-
[[2wyy]] – VvNP + poly U – Cryo EM<br />
+
-
[[3hhw]], [[3pmk]] – VvNP + phosphoprotein<br />
+
-
[[3hhz]] - VvNP + phosphoprotein + RNA<br />
+
-
[[2wj8]], [[2yhm]] – NP + RNA – Human respiratory syncytial virus<br />
+
-
[[2i91]], [[1yvp]] – XlNP Ro + RNA <br />
+
-
[[2gtt]] – NP + RNA – Rabies virus<br />
+
-
[[1wwg]], [[1wwd]], [[1wwe]], [[1u6p]] - MvNP P10 + RNA – NMR<br />
+
-
[[3ro5]] – IvNP + ligand<br />
+
-
[[4bbl]] – IvNP + RNA – Cryo EM
+
-
 
+
-
===Ribonucleoprotein===
+
-
 
+
-
[[2lbw]] – yRNP subunit 2 residues 36-156 (mutant) – yeast – NMR<br />
+
-
[[2lbx]] - yRNP subunit 2 residues 36-156 – NMR<br />
+
-
 
+
-
===Small nuclear ribonucleoprotein===
+
-
 
+
-
[[2a3j]], [[1fht]] - h-snRNP U1 A RRM – human - NMR<br />
+
-
[[2u1a]] - h-snRNP U1 A RRM (mutant) – NMR<br />
+
-
[[1oia]] - h-snRNP U1 A RRM<br />
+
-
[[2l5i]], [[2l5j]] - h-snRNP U1 70kDa residues 131-151 – NMR<br />
+
-
[[2vy4]], [[2vy5]] - h-snRNP U11/U12 – NMR<br />
+
-
[[2cqj]] - h-snRNP U3 S4 domain – NMR<br />
+
-
[[1x4q]] - h-snRNP U4/U6 PWI domain - NMR<br />
+
-
[[2vrd]] - h-snRNP U1 C zinc finger domain - NMR<br />
+
-
[[1b34]] - h-snRNP D1 + h-snRNP D2<br />
+
-
[[2k3k]] – Dm-snRNP U1 A RRM1 – ''Drosophila melanogaster'' – NMR<br />
+
-
[[2aym]] - Dm-snRNP U1 A<br />
+
-
[[2b0g]] - Dm-snRNP U1 A RBD2 – NMR<br />
+
-
[[1n9r]], [[1n9s]] – y-snRNP F
+
-
 
+
-
===Small nuclear ribonucleoprotein binary complex===
+
-
 
+
-
[[3plu]], [[3plv]] – y-snRNP HINDI domain + ubiquitin-like modifier HUB1<br />
+
-
[[2y9a]], [[2y9b]], [[2y9c]], [[2y9d]] – h-snRNP U4 core domain<br />
+
-
[[3p49]] - h-snRNP A RRM + glycine riboswitch RNA<br />
+
-
[[3iwn]] - h-snRNP U1 A RRM (mutant) + riboswitch RNA<br />
+
-
[[3pgw]], [[3mum]], [[3mur]], [[3mut]], [[3muv]], [[3egz]] - h-snRNP U1 A + DNA riboswitch<br />
+
-
[[3mxh]], [[3irw]] - h-snRNP U1 A (mutant) + DNA riboswitch<br />
+
-
[[3k0j]], [[1drz]], [[1m5k]], [[1m5o]], [[1m5p]], [[1m5v]], [[1u6b]] - h-snRNP U1 A (mutant) + RNA<br />
+
-
[[3bo2]], [[3bo3]], [[3bo4]] - h-snRNP U1 A RRM + RNA<br />
+
-
[[1sj3]], [[1sj4]], [[1sjf]], [[1vbx]], [[1vby]], [[1vbz]], [[1vc0]], [[1vc5]], [[1vc6]], [[1vc7]] - h-snRNP U1 A (mutant) + Hepatitis ribozyme<br />
+
-
[[3r1h]], [[3r1l]] - h-snRNP U1 A (mutant) + ribozyme<br />
+
-
[[1aud]] - h-snRNP U1 A (mutant) + RNA - NMR<br />
+
-
[[3iin]] - h-snRNP U1 A (mutant) + group I intron + DNA<br />
+
-
[[3b02]], [[3b03]], [[3b04]] - h-snRNP U1 A RRM1 + group I intron + RNA<br />
+
-
[[1zzn]] - h-snRNP U1 A RRM1 (mutant) + group I intron + RNA<br />
+
-
[[3l3c]], [[3g8s]], [[3g8t]], [[3g96]], [[3g9c]], [[2nz4]] - h-snRNP U1 A (mutant) + GLMS ribozyme + RNA<br />
+
-
[[3hhn]] - h-snRNP U1 A (mutant) + class I ligase ribozyme<br />
+
-
[[2oih]], [[2oj3]] - h-snRNP U1 A + HDV ribozyme<br />
+
-
[[3cul]], [[3cun]] - h-snRNP U1 A (mutant) + aminoacyl-tRNA synthetase ribozyme<br />
+
-
[[3cw1]] - h-snRNP U1 in spliceosome<br />
+
-
[[2ozb]], [[3siu]], [[3siv]] - h-snRNP U4/U6 + NHP2-like protein + RNA<br />
+
-
[[3s6n]] - h-snRNP D1 + h-snRNP D2 + h-snRNP E + h-snRNP F + h-snRNP G + survival motor neuron protein + SMN interacting protein<br />
+
-
[[2bn5]] - Dm-snRNP U1 70kDa + PSI B box – NMR<br />
+
-
 
+
-
===Heterogenous nuclear ribonucleoprotein===
+
-
 
+
-
[[3s01]] – m-hnRNP L RRM3 domain – mouse<br />
+
-
[[3tyt]] - m-hnRNP L<br />
+
-
[[2e5i]] - m-hnRNP L RRM – NMR<br />
+
-
[[2db1]] - m-hnRNP F RRM – NMR<br />
+
-
[[1ha1]], [[1l3k]], [[1up1]] - h-hnRNP A1 RRM<br />
+
-
[[3s7r]] - h-hnRNP A/B<br />
+
-
[[1x4b]] - h-hnRNP A2/B1 RRM – NMR<br />
+
-
[[1txp]] - h-hnRNP C oligomerization domain – NMR<br />
+
-
[[1wf2]] - h-hnRNP C1/C2 RRM – NMR<br />
+
-
[[1hd0]], [[1hd1]], [[1iqt]] - h-hnRNP D0 RRM – NMR<br />
+
-
[[2hgl]], [[2hgm]], [[2hgn]] - h-hnRNP F QRRM – NMR<br />
+
-
[[1wg5]], [[1wez]] - h-hnRNP H RRM – NMR<br />
+
-
[[2ad9]], [[2adb]], [[2adc]] - h-hnRNP I – NMR<br />
+
-
[[1zzk]] - h-hnRNP K KH domain<br />
+
-
[[3r27]], [[3t08]] - h-hnRNP L RRM<br />
+
-
[[2do0]], [[2dh9]], [[2dgv]] - h-hnRNP M RRM – NMR<br />
+
-
[[2dgu]] - h-hnRNP Q RRM – NMR<br />
+
-
[[2dk2]] - h-hnRNP R RRM – NMR<br />
+
-
 
+
-
===Heterogenous nuclear ribonucleoprotein binary complex===
+
-
 
+
-
[[2kfy]], [[2kg0]], [[2kg1]] - h-hnRNP F QRRM + DNA – NMR<br />
+
-
[[2z5n]], [[2z5o]], [[2ot8]] - h-hnRNP D0 CTD + transportin-1<br />
+
-
[[1u1k]], [[1u1l]], [[1u1m]], [[1u1n]], [[1u1o]], [[1u1p]], [[1u1q]], [[1u1r]], [[1up1]] - h-hnRNP A1 RRM + DNA<br />
+
-
[[1pgz]], [[1po6]] - h-hnRNP A1 + DNA + inhibitor<br />
+
-
[[1wtb]], [[1x0f]] - h-hnRNP D0 RRM + DNA – NMR<br />
+
-
[[1zzi]], [[1zzj]] - h-hnRNP K KH domain + DNA<br />
+
-
[[1j5k]] - h-hnRNP K KH domain + DNA – NMR
+
 +
== References ==
 +
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

Nucleoprotein from Lassa virus trimer complex with TTP and Zn+2 ions (grey) 3mx2

Drag the structure with the mouse to rotate

References

  1. ↑ Echols H. Nucleoprotein structures initiating DNA replication, transcription, and site-specific recombination. J Biol Chem. 1990 Sep 5;265(25):14697-700. PMID:2203758
  2. ↑ Yong J, Wan L, Dreyfuss G. Why do cells need an assembly machine for RNA-protein complexes? Trends Cell Biol. 2004 May;14(5):226-32. PMID:15130578 doi:http://dx.doi.org/10.1016/j.tcb.2004.03.010
  3. ↑ He Y, Smith R. Nuclear functions of heterogeneous nuclear ribonucleoproteins A/B. Cell Mol Life Sci. 2009 Apr;66(7):1239-56. doi: 10.1007/s00018-008-8532-1. PMID:19099192 doi:http://dx.doi.org/10.1007/s00018-008-8532-1

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Jaime Prilusky, Joel L. Sussman

Retrieved from "http://52.214.119.220/wiki/index.php/Nucleoprotein"
Personal tools