7NWU: Regulator of nonsense transcripts 3B
Co-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII. Determined by X-ray diffraction at 2.6 Å resolution. Released 20 Jul 2022.
- Method
- X-ray diffraction
- Resolution
- 2.6 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 12,248
- Mol. weight
- 177.44 kDa
- Released
- 20 Jul 2022
Explore 7NWU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7NWU contains 94 α-helices and 24 β-strands across 8 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.
Chain A: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 52-58 | 7 | 1 |
| α-helix | 64-71 | 8 | |
| α-helix | 72 | 1 | |
| α-helix | 74 | 1 | |
| β-strand | 77-84 | 8 | 1 |
| β-strand | 95-101 | 7 | 1 |
| α-helix | 105-114 | 10 | |
| α-helix | 117 | 1 | |
| β-strand | 118-120 | 3 | 2 |
| β-strand | 126-128 | 3 | 2 |
| β-strand | 130-133 | 4 | 1 |
| α-helix | 146-148 | 3 | |
| α-helix | 154-156 | 3 | |
| α-helix | 158-166 | 9 | |
Chain B: 18 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 770-777 | 8 | |
| α-helix | 778-782 | 5 | |
| α-helix | 783-785 | 3 | |
| α-helix | 788-795 | 8 | |
| α-helix | 803-814 | 12 | |
| α-helix | 816-818 | 3 | |
| α-helix | 821-823 | 3 | |
| α-helix | 824-834 | 11 | |
| α-helix | 839-859 | 21 | |
| α-helix | 862-864 | 3 | |
| α-helix | 865-880 | 16 | |
| α-helix | 886-896 | 11 | |
| α-helix | 917-929 | 13 | |
| α-helix | 930-932 | 3 | |
| α-helix | 937-957 | 21 | |
| α-helix | 967-969 | 3 | |
| α-helix | 970-983 | 14 | |
| α-helix | 993-1011 | 19 | |
Chain C: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 52-58 | 7 | 3 |
| α-helix | 64-71 | 8 | |
| α-helix | 72 | 1 | |
| α-helix | 74 | 1 | |
| β-strand | 77-84 | 8 | 3 |
| β-strand | 95-101 | 7 | 3 |
| α-helix | 105-114 | 10 | |
| β-strand | 118-120 | 3 | 4 |
| β-strand | 126-128 | 3 | 4 |
| β-strand | 130-133 | 4 | 3 |
| α-helix | 158-168 | 11 | |
Chain D: 17 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 770-780 | 11 | |
| α-helix | 782-784 | 3 | |
| α-helix | 788-793 | 6 | |
| α-helix | 803-814 | 12 | |
| α-helix | 816-818 | 3 | |
| α-helix | 821-823 | 3 | |
| α-helix | 824-834 | 11 | |
| α-helix | 839-859 | 21 | |
| α-helix | 862-864 | 3 | |
| α-helix | 865-880 | 16 | |
| α-helix | 886-898 | 13 | |
| α-helix | 917-929 | 13 | |
| α-helix | 930-932 | 3 | |
| α-helix | 937-957 | 21 | |
| α-helix | 967-969 | 3 | |
| α-helix | 970-983 | 14 | |
| α-helix | 993-1011 | 19 | |
Chain E: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 52-58 | 7 | 5 |
| α-helix | 64-71 | 8 | |
| α-helix | 72 | 1 | |
| α-helix | 74-76 | 3 | |
| β-strand | 77-84 | 8 | 5 |
| β-strand | 95-101 | 7 | 5 |
| α-helix | 105-114 | 10 | |
| β-strand | 118-120 | 3 | 6 |
| β-strand | 126-128 | 3 | 6 |
| β-strand | 130-133 | 4 | 5 |
| α-helix | 158-167 | 10 | |
Chain F: 18 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 770-777 | 8 | |
| α-helix | 778-782 | 5 | |
| α-helix | 783-785 | 3 | |
| α-helix | 788-795 | 8 | |
| α-helix | 803-814 | 12 | |
| α-helix | 816-818 | 3 | |
| α-helix | 821-823 | 3 | |
| α-helix | 824-834 | 11 | |
| α-helix | 839-859 | 21 | |
| α-helix | 862-864 | 3 | |
| α-helix | 865-880 | 16 | |
| α-helix | 886-898 | 13 | |
| α-helix | 917-929 | 13 | |
| α-helix | 930-932 | 3 | |
| α-helix | 937-957 | 21 | |
| α-helix | 967-969 | 3 | |
| α-helix | 970-983 | 14 | |
| α-helix | 993-1011 | 19 | |
Chain G: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 52-58 | 7 | 7 |
| α-helix | 64-71 | 8 | |
| α-helix | 72 | 1 | |
| α-helix | 74-75 | 2 | |
| β-strand | 77-84 | 8 | 7 |
| β-strand | 95-101 | 7 | 7 |
| α-helix | 105-114 | 10 | |
| β-strand | 118-120 | 3 | 8 |
| β-strand | 126-128 | 3 | 8 |
| β-strand | 130-133 | 4 | 7 |
| α-helix | 158-168 | 11 | |
Chain H: 18 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 770-777 | 8 | |
| α-helix | 778-782 | 5 | |
| α-helix | 783-785 | 3 | |
| α-helix | 788-796 | 9 | |
| α-helix | 803-814 | 12 | |
| α-helix | 816-818 | 3 | |
| α-helix | 821-823 | 3 | |
| α-helix | 824-834 | 11 | |
| α-helix | 839-859 | 21 | |
| α-helix | 862-864 | 3 | |
| α-helix | 865-880 | 16 | |
| α-helix | 886-898 | 13 | |
| α-helix | 917-929 | 13 | |
| α-helix | 930-932 | 3 | |
| α-helix | 936-957 | 22 | |
| α-helix | 967-969 | 3 | |
| α-helix | 970-983 | 14 | |
| α-helix | 993-1011 | 19 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Regulator of nonsense transcripts 3B | A, C, E, G | protein | 122 | Homo sapiens | Q9BZI7 (AlphaFold model) |
| Regulator of nonsense transcripts 2 | B, D, F, H | protein | 251 | Homo sapiens | Q9HAU5 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G), FASTA
>7NWU_1 Regulator of nonsense transcripts 3B (chains A, C, E, G)
ALSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDII
LFRDRFDGYVFLDNKGQEYPAIVEFAPFQKAAKKKTKKRDTKVGTIDDDPEYRKFLESYA
TD
Sequence of entity 2 (B, D, F, H), FASTA
>7NWU_2 Regulator of nonsense transcripts 2 (chains B, D, F, H)
KRPPLQEYVRKLLYKDLSKVTTEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHC
VANLLAGLVLYQEDVGIHVVDGVLEDIRLGMEVNQPKFNQRRISSAKFLGELYNYRMVES
AVIFRTLYSFTSFGVNPDGSPSSLDPPEHLFRIRLVCTILDTCGQYFDRGSSKRKLDCFL
VYFQRYVWWKKSLEVWTKDHPFPIDIDYMISDTLELLRPKIKLCNSLEESIRQVQDLERE
FLIKLGLVNDK
Primary citation
Structures of nonsense-mediated mRNA decay factors UPF3B and UPF3A in complex with UPF2 reveal molecular basis for competitive binding and for neurodevelopmental disorder-causing mutation. Bufton, J.C., Powers, K.T., Szeto, J.A. et al. Nucleic Acids Res (2022) 50:5934-5947. DOI 10.1093/nar/gkac421 · PubMed
Other PDB entries of the same protein (UniProt Q9BZI7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1UW4 1.95 Å, The structural basis of the interaction between nonsense mediated decay factors UPF2 and…
- 2XB2 3.4 Å, Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the…
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