V(D)J recombination-activating protein 1 (Rag1) is a 1040-residue protein from Mus musculus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P15919.
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The mean pLDDT of this model is 81.4 (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 | 59% |
| 70 to 90 | Confident: backbone generally right | 21% |
| 50 to 70 | Low: treat with caution | 4% |
| Below 50 | Very low: often disordered regions | 17% |
What pLDDT means and how to read it
Catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D (diversity), and J (joining) gene segments. In the RAG complex, RAG1 mediates the DNA-binding to the conserved recombination signal sequences (RSS) and catalyzes the DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. RAG2 is not a catalytic component but is required for all known catalytic activities. DNA cleavage…
Homodimer. Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2. Interacts with DCAF1, leading to recruitment of the CUL4A-RBX1-DDB1-DCAF1/VPRBP complex to ubiquitinate proteins and limit error-prone repair during V(D)J recombination
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1RMD | X-ray | 2.1 Å | A=265-380 |
| 3GNA | X-ray | 2.4 Å | A=389-464 |
| 6XNX | EM | 2.7 Å | A/C=261-1008 |
| 5ZE0 | X-ray | 2.75 Å | A/C=384-1008 |
| 5ZDZ | X-ray | 2.8 Å | A/C=384-1008 |
| 6XNY | EM | 2.9 Å | A/C=261-1008 |
| 9JPX | EM | 2.95 Å | A/C=1-1040 |
| 3GNB | X-ray | 3.0 Å | A=389-464 |
| 5ZE1 | X-ray | 3.0 Å | A/C=384-1008 |
| 9JQN | EM | 3.03 Å | A/C=1-1040 |
| 6OES | EM | 3.06 Å | A/C=1-1040 |
| 6CIK | X-ray | 3.15 Å | A/C=384-1008 |
| 6CG0 | EM | 3.17 Å | A/C=265-1039 |
| 4WWX | X-ray | 3.2 Å | B/E=392-1008 |
| 9JPU | EM | 3.25 Å | A/C=1-1040 |
| 6OER | EM | 3.29 Å | A/C=1-1040 |
| 5ZE2 | X-ray | 3.3 Å | A/C=384-1008 |
| 9JTS | EM | 3.36 Å | A/C=1-1040 |
| 6OET | EM | 3.4 Å | A/C=1-1040 |
| 9JTU | EM | 3.43 Å | A/C=1-1040 |
Showing 20 of 30 experimental structures (best resolution first).
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