Nucleoprotein

From Proteopedia

Revision as of 10:42, 6 December 2011

Template:STRUCTURE 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). For homology model and multiple sequence alignment see User:Michael Strong/H1N1/NP and User:Michael Strong/H1N1/NP/MSA.

3D Structures of Nucleoprotein

Updated December 2011

Nucleoprotein

3ouo, 3ov9 – NP – Rift valley fever virus
3q7b, 3q7c, 3mwp, 3mwt – LvNP exonuclease domain – Lassa virus
3pto - VvNP – Vesicular stomatitis Indiana virus
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

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, 1fht - h-snRNP U1 A RRM – human - NMR
2u1a - h-snRNP U1 A RRM (mutant) – NMR
1oia - h-snRNP U1 A RRM
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
1b34 - h-snRNP D1 + h-snRNP D2
2k3k – Dm-snRNP U1 A RRM1 – Drosophila melanogaster – NMR
2aym - Dm-snRNP U1 A
2b0g - Dm-snRNP U1 A RBD2 – NMR
1n9r, 1n9s – y-snRNP F

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
3iwn - h-snRNP U1 A RRM (mutant) + riboswitch RNA
3pgw, 3mum, 3mur, 3mut, 3muv, 3egz - h-snRNP U1 A + DNA riboswitch
3mxh, 3irw - h-snRNP U1 A (mutant) + DNA riboswitch
3k0j, 1drz, 1m5k, 1m5o, 1m5p, 1m5v, 1u6b - h-snRNP U1 A (mutant) + RNA
3bo2, 3bo3, 3bo4 - h-snRNP U1 A RRM + RNA
1sj3, 1sj4, 1sjf, 1vbx, 1vby, 1vbz, 1vc0, 1vc5, 1vc6, 1vc7 - h-snRNP U1 A (mutant) + Hepatitis ribozyme
3r1h, 3r1l - h-snRNP U1 A (mutant) + ribozyme
[[1aud - h-snRNP U1 A (mutant) + RNA - NMR
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, 3siu, 3siv - h-snRNP U4/U6 + NHP2-like protein + RNA
3s6n - h-snRNP D1 + h-snRNP D2 + h-snRNP E + h-snRNP F + h-snRNP G + survival motor neuron protein + SMN interacting protein
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
1ha1, 1l3k, 1up1 - h-hnRNP A1 RRM
3s7r - h-hnRNP A/B
1x4b - h-hnRNP A2/B1 RRM – NMR
1txp - h-hnRNP C oligomerization domain – NMR
1wf2 - h-hnRNP C1/C2 RRM – NMR
1hd0, 1hd1, 1iqt - h-hnRNP D0 RRM – NMR
2hgl, 2hgm, 2hgn - h-hnRNP F QRRM – NMR
1wg5, 1wez - h-hnRNP H RRM – NMR
2ad9, 2adb, 2adc - h-hnRNP I – NMR
1zzk - h-hnRNP K KH domain
3r27 - h-hnRNP L RRM
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

2kfy, 2kg0, 2kg1 - h-hnRNP F QRRM + DNA – NMR
2z5n, 2z5o, 2ot8 - h-hnRNP D0 CTD + transportin-1
1u1k, 1u1l, 1u1m, 1u1n, 1u1o, 1u1p, 1u1q, 1u1r, 1up1 - h-hnRNP A1 RRM + DNA
1pgz, 1po6 - h-hnRNP A1 + DNA + inhibitor
1wtb, 1x0f - h-hnRNP D0 RRM + DNA – NMR
1zzi, 1zzj - h-hnRNP K KH domain + DNA
1j5k - h-hnRNP K KH domain + DNA – NMR