Protein transport protein SEC13 (SEC13) is a 297-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q04491.
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The mean pLDDT of this model is 92.3 (very high 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 | 83% |
| 70 to 90 | Confident: backbone generally right | 13% |
| 50 to 70 | Low: treat with caution | 2% |
| Below 50 | Very low: often disordered regions | 3% |
What pLDDT means and how to read it
Functions as a component of the nuclear pore complex (NPC) and the COPII coat. It is one of 5 proteins constituting the COPII coat, which is involved in anterograde (ER to Golgi) double-membrane transport vesicle formation. First the small GTPase SAR1, activated by and binding to the integral ER membrane protein SEC12, exchanges GDP for GTP and recruits the heterodimer SEC23/24, which in turn recruits the heterotetramer SEC13-SEC31. The polymerization of COPII coat complexes then causes physically the deformation (budding) of the membrane, leading to the creation of a transport vesicle. The COPII complex is dissociated upon SAR1-GTP hydrolysis to SAR1-GDP. SEC23 functions as the SAR1…
The basic repeat unit of a COPII coated vesicle is composed of 5 proteins: the small GTPase SAR1, the heterodimeric SEC23-SEC24 complex, and the heterotetrameric SEC13-SEC31 complex. This repeat unit polymerizes to induce membrane deformation into a transport vesicle. Component of the nuclear pore complex (NPC). NPC constitutes the exclusive means of nucleocytoplasmic transport. NPCs allow the…
Cytoplasmic vesicle, COPII-coated vesicle membrane, Endoplasmic reticulum membrane, Nucleus, nuclear pore complex, Vacuole membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2PM7 | X-ray | 2.35 Å | B/D=1-297 |
| 2PM6 | X-ray | 2.45 Å | B/D=1-297 |
| 3JRP | X-ray | 2.6 Å | A=1-297 |
| 3MZK | X-ray | 2.69 Å | A/D=1-297 |
| 3MZL | X-ray | 2.8 Å | A/C/E/G=1-297 |
| 8ADL | EM | 2.95 Å | H/P=1-297 |
| 3IKO | X-ray | 3.2 Å | A/D/G=1-297 |
| 9H5K | EM | 3.2 Å | H/P=1-297 |
| 2PM9 | X-ray | 3.3 Å | B=1-297 |
| 3JRO | X-ray | 4.0 Å | A=1-297 |
| 4XMM | X-ray | 7.38 Å | A=1-297 |
| 4XMN | X-ray | 7.6 Å | A=1-297 |
| 8TIE | EM | 8.1 Å | d/o=1-297 |
| 7N84 | EM | 11.6 Å | d/o=1-297 |
| 7N9F | EM | 37.0 Å | d/k=1-297 |
| 4BZJ | EM | 40.0 Å | B/F=2-292 |
| 4BZK | EM | 40.0 Å | B/F=1-297 |
| 6ZG5 | EM | 40.0 Å | B/F=1-297 |
| 6ZG6 | EM | 40.0 Å | B/D/F/H=1-297 |
| 6ZL0 | EM | 40.0 Å | B/D=1-297 |
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