HLA class II histocompatibility antigen gamma chain (CD74) is a 296-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P04233.
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The mean pLDDT of this model is 69.9 (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 | 26% |
| 70 to 90 | Confident: backbone generally right | 28% |
| 50 to 70 | Low: treat with caution | 19% |
| Below 50 | Very low: often disordered regions | 27% |
What pLDDT means and how to read it
Plays a critical role in MHC class II antigen processing by stabilizing peptide-free class II alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to the endosomal/lysosomal system where the antigen processing and binding of antigenic peptides to MHC class II takes place. Serves as cell surface receptor for the cytokine MIF
Homotrimer. In the endoplasmic reticulum (ER) it forms a heterononameric MHC II-Ii complex: 3 MHC class II molecules (heterodimers of an alpha and a beta subunit) bind to the CD74 homotrimer (also known as invariant chain or HLA class II histocompatibility antigen gamma chain). In the endosomal/lysosomal system, the CD74 component undergoes sequential degradation by various proteases, including…
Cell membrane, Endoplasmic reticulum membrane, Golgi apparatus, trans-Golgi network, Endosome, Lysosome, Secreted, Late endosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4X5W | X-ray | 1.34 Å | C=102-120 |
| 7YX9 | X-ray | 1.76 Å | E/G=103-117 |
| 3PDO | X-ray | 1.95 Å | C=102-120 |
| 1ICF | X-ray | 2.0 Å | I/J=210-274 |
| 7YXB | X-ray | 2.1 Å | G/H=103-117 |
| 7Z0Q | X-ray | 2.1 Å | G=103-117 |
| 1MUJ | X-ray | 2.15 Å | C=97-122 |
| 5KSV | X-ray | 2.19 Å | C=109-123 |
| 4AEN | X-ray | 2.2 Å | C=106-120 |
| 8VSJ | EM | 2.28 Å | P=103-117 |
| 3QXD | X-ray | 2.3 Å | C/F=103-117 |
| 4AH2 | X-ray | 2.36 Å | B=106-120 |
| 9EJH | X-ray | 2.45 Å | C=110-122 |
| 3PGC | X-ray | 2.66 Å | C/F=106-120 |
| 3QXA | X-ray | 2.71 Å | C/F=103-117 |
| 3PGD | X-ray | 2.72 Å | C/F=106-120 |
| 5KSU | X-ray | 2.73 Å | C/F=103-117 |
| 1A6A | X-ray | 2.75 Å | C=103-117 |
| 8VRW | EM | 3.03 Å | C/F/I=2-296 |
| 8VSP | EM | 3.12 Å | C/F/I=2-296 |
Showing 20 of 24 experimental structures (best resolution first).
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