Nuclear pore complex protein Nup98-Nup96 (NUP98) is a 1817-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P52948.
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The mean pLDDT of this model is 55.7 (low overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 5% |
| 70 to 90 | Confident: backbone generally right | 34% |
| 50 to 70 | Low: treat with caution | 10% |
| Below 50 | Very low: often disordered regions | 52% |
What pLDDT means and how to read it
Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance. NUP98 and NUP96 are involved in the bidirectional transport across the NPC (PubMed:33097660). May anchor NUP153 and TPR to the NPC. In cooperation with DHX9, plays a role in transcription and alternative splicing activation of a subset of genes (PubMed:28221134). Involved in the localization of DHX9 in discrete intranuclear foci (GLFG-body) (PubMed:28221134)
Part of the nuclear pore complex (NPC) (PubMed:15229283, PubMed:18287282). Interacts directly with NUP96 (PubMed:12191480). Part of the Nup160 subcomplex in the nuclear pore which is composed of NUP160, NUP133, NUP107 and NUP96; this complex plays a role in RNA export and in tethering NUP98 and NUP153 to the nucleus (PubMed:11684705). Interacts with RAE1 (PubMed:10209021, PubMed:20498086). Does…
Nucleus membrane, Nucleus, nuclear pore complex, Nucleus, nucleoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6BZM | EM | 0.9 Å | A/B=116-123 |
| 3MMY | X-ray | 1.65 Å | B/D/F/H=158-213 |
| 2Q5X | X-ray | 1.9 Å | A=733-887 |
| 7MNI | X-ray | 2.0 Å | B/D=732-880 |
| 2Q5Y | X-ray | 2.3 Å | A/C=729-880 |
| 7F90 | X-ray | 2.39 Å | B/D=1-1817 |
| 7VPG | X-ray | 2.49 Å | B/D/F/H=158-213 |
| 8CI8 | EM | 2.67 Å | A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y=298-327 |
| 7Q64 | EM | 2.76 Å | A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y/Z/a/b/c/d=85-124 |
| 7Q66 | EM | 2.79 Å | A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V=85-124 |
| 7VPH | X-ray | 2.8 Å | B/D/F/H=158-213 |
| 7F60 | X-ray | 2.85 Å | C/D=1-1817 |
| 1KO6 | X-ray | 3.0 Å | A/C=695-880, B/D=881-941 |
| 4OWR | X-ray | 3.15 Å | B=157-213 |
| 7Q65 | EM | 3.32 Å | A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V=85-124 |
| 7Q67 | EM | 3.37 Å | A/B/C/D/E/F/G/H/I/J/K=85-124 |
| 7R5K | EM | 12.0 Å | M0/M1/M2/M3=881-1817, U0/U1/U2/U3/U4/U5/U6=1-880 |
| 5A9Q | EM | 23.0 Å | 5/E/N/W=881-1817 |
| 7PEQ | EM | 35.0 Å | AE/BE/CE/DE=881-1817 |
| 7R5J | EM | 50.0 Å | M0/M1/M2/M3=881-1817, U0/U1/U2/U3/U4/U5/U6=1-880 |
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