Structure of Rhizobium NopD with ubiquitin. Determined by X-ray diffraction at 1.94 Å resolution. Released 20 Nov 2024.
Explore 8RQI in 3D Show helices and sheets RCSB PDB PDBe
8RQI contains 14 α-helices and 16 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 835-837 | 3 | |
| β-strand | 838 | 1 | 1 |
| α-helix | 839-856 | 18 | |
| α-helix | 858-862 | 5 | |
| β-strand | 864-866 | 3 | 2 |
| α-helix | 869-875 | 7 | |
| α-helix | 880-890 | 11 | |
| α-helix | 892-894 | 3 | |
| β-strand | 897-903 | 7 | 2 |
| β-strand | 917-923 | 7 | 2 |
| β-strand | 931-935 | 5 | 2 |
| α-helix | 943-952 | 10 | |
| β-strand | 956-960 | 5 | 2 |
| β-strand | 962 | 1 | 3 |
| α-helix | 963-965 | 3 | |
| α-helix | 971-987 | 17 | |
| β-strand | 995 | 1 | 3 |
| α-helix | 1002-1010 | 9 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-6 | 5 | 4 |
| β-strand | 12-16 | 5 | 4 |
| β-strand | 22 | 1 | 5 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 4 |
| β-strand | 48-49 | 2 | 4 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 5 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 4 |
| β-strand | 74 | 1 | 1 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| NopD | A | protein | 246 | Bradyrhizobium | A0ABV4GMV7 |
| Polyubiquitin-B | B | protein | 75 | Homo sapiens | F5H388 (AlphaFold model) |
>8RQI_1 NopD (chains A) MGSSHHHHHHSSGLVPRGSHGPRGRRVAQFIHHPRPSPVPGAQIGPSATVASSGHRSGPV LGPTQWLGDEHIQRDYELLAQELQQNNPDLAARTRFVDPLIAQMLRSPSKEVAERALGWV RPGTADFLFLPVSDASDTDRHQRGSHWSLLLVDRRDRGRRVAYHYDSTQGYNDGLAAELA GRLDANLQQAPIRQQQNSYDCGVFVLDGTRELVRRLAARRPDLNLNNLVISRQELRDRLG AGVGFN
>8RQI_2 Polyubiquitin-B (chains B) MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRG
| ID | Name | Formula | Copies |
|---|---|---|---|
| AYE | prop-2-en-1-amine | C3 H7 N | 1 |
Broad-spectrum ubiquitin/ubiquitin-like deconjugation activity of the rhizobial effector NopD from Bradyrhizobium (sp. XS1150). Li, Y., Perez-Gil, J., Lois, L.M. et al. Commun Biol (2024) 7:644-644. DOI 10.1038/s42003-024-06344-w · PubMed
Other PDB entries of the same protein (UniProt A0ABV4GMV7), best resolution first:
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