The model was generated using AlphaFold 2.
Using DeepTMHMM, this protein was identified to contain a signal peptide and a transmembrane domain.
The transmembrane domain spans residues: 680-702
EBV_BXLF2-nosignal_rank_001.pdb
EBV_BXLF2-nosignal_rank_002.pdb
EBV_BXLF2-nosignal_rank_003.pdb
EBV_BXLF2-nosignal_rank_004.pdb
EBV_BXLF2-nosignal_rank_005.pdb
This page uses 3Dmol.js: Molecular visualization with WebGL by Nicholas Rego and David Koes. Bioinformatics (2015) doi: 10.1093/bioinformatics/btu829
Predictions were run with Colabfold by the Steinegger lab:
Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. “ColabFold: Making protein folding accessible to all”.
Nature Methods (2022) doi: 10.1038/s41592-022-01488-1
Foldseek is developed by the Steinegger lab:
van Kempen M, Kim S, Tumescheit C, Mirdita M, Söding J, and Steinegger M. “Fast and accurate protein structure search with Foldseek”.
Nature Biotechnology (2023) doi: 10.1038/s41587-023-01773-0
Alphafold2 was developed by Deepmind:
Jumper et al. “Highly accurate protein structure prediction with AlphaFold.”
Nature (2021) doi: 10.1038/s41586-021-03819-2
Signal peptide predictions were performed with DeepTMHMM
Jeppe Hallgren, Konstantinos D. Tsirigos, Mads Damgaard Pedersen, José Juan Almagro Armenteros, Paolo Marcatili, Henrik Nielsen, Anders Krogh, Ole Winther.
“DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks.”
bioRxiv (2022) doi: 10.1101/2022.04.08.487609
AlphaFold3 models were generated through the Alphafold Server, which uses Google DeepMind’s AlphaFold technology
Abramson J, et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature (2024).
doi: 10.1038/s41586-024-07487-w