Mediator of RNA polymerase II transcription subunit 3 (PGD1) is a 397-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P40356.
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The mean pLDDT of this model is 52.6 (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 | 1% |
| 70 to 90 | Confident: backbone generally right | 18% |
| 50 to 70 | Low: treat with caution | 20% |
| Below 50 | Very low: often disordered regions | 60% |
What pLDDT means and how to read it
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. The Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the…
Component of the Mediator complex, which is composed of at least 21 subunits that form three structurally distinct submodules. The Mediator head module contains MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22, the middle module contains MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31, and the tail module contains MED2, PGD1/MED3,…
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7UIO | EM | 3.3 Å | Ac/Bc=1-397 |
| 7UIC | EM | 3.7 Å | c=1-397 |
| 7UIL | EM | 4.3 Å | 2/c=1-397 |
| 7UIK | EM | 7.7 Å | c=1-397 |
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