Protein translocase subunit SecY (secY) is a 430-residue protein from Geobacillus thermodenitrificans (strain NG80-2). This is its AlphaFold structure prediction, created 1 Jun 2022. UniProt accession: A4IJK8.
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The mean pLDDT of this model is 80.1 (confident 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 | 19% |
| 70 to 90 | Confident: backbone generally right | 61% |
| 50 to 70 | Low: treat with caution | 18% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently
Component of the Sec protein translocase complex. Heterotrimer consisting of SecY, SecE and SecG subunits. The heterotrimers can form oligomers, although 1 heterotrimer is thought to be able to translocate proteins. Interacts with the ribosome. Interacts with SecDF, and other proteins may be involved. Interacts with SecA
Cell membrane, Membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8YA0 | EM | 2.97 Å | Y=2-430 |
| 8YA3 | EM | 3.27 Å | Y=1-430 |
| 8Y9Y | EM | 3.29 Å | Y=1-430 |
| 7XHB | EM | 3.33 Å | Y=1-430 |
| 7XHA | EM | 3.35 Å | Y=1-430 |
| 8Y9Z | EM | 3.41 Å | Y=1-430 |
| 6ITC | EM | 3.45 Å | Y=1-430 |
| 5EUL | X-ray | 3.7 Å | Y=1-430 |
| 8YA2 | EM | 3.84 Å | Y=1-430 |
| 8YAS | EM | 3.97 Å | Y=1-430 |
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