5WMF: Epstein-Barr nuclear antigen 1
Crystal structure of the Hexameric Ring of Epstein-Barr Virus Nuclear Antigen-1, EBNA1. Determined by X-ray diffraction at 1.9 Å resolution. Released 9 Aug 2017.
- Method
- X-ray diffraction
- Resolution
- 1.9 Å
- Organism
- Epstein-Barr virus
- Chains
- 6
- Atoms
- 6,712
- Mol. weight
- 99.71 kDa
- Released
- 9 Aug 2017
Explore 5WMF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5WMF contains 44 α-helices and 30 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 8 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 478-489 | 12 | |
| β-strand | 503-511 | 9 | 1 |
| α-helix | 514-527 | 14 | |
| β-strand | 532-533 | 2 | 1 |
| α-helix | 534-536 | 3 | |
| β-strand | 537-540 | 4 | 1 |
| α-helix | 550-552 | 3 | |
| β-strand | 556-566 | 11 | 1 |
| α-helix | 569-583 | 15 | |
| α-helix | 587 | 1 | |
| α-helix | 590-592 | 3 | |
| β-strand | 593-604 | 12 | 1 |
| α-helix | 606-608 | 3 | |
Chain B: 8 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 476-489 | 14 | |
| β-strand | 505-511 | 7 | 1 |
| α-helix | 514-527 | 14 | |
| β-strand | 532-533 | 2 | 1 |
| α-helix | 534-536 | 3 | |
| β-strand | 537-540 | 4 | 1 |
| α-helix | 541 | 1 | |
| α-helix | 543-544 | 2 | |
| β-strand | 556-566 | 11 | 1 |
| α-helix | 569-584 | 16 | |
| α-helix | 587 | 1 | |
| α-helix | 590-592 | 3 | |
| β-strand | 593-600 | 8 | 1 |
Chain C: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 477-489 | 13 | |
| β-strand | 503-511 | 9 | 2 |
| α-helix | 514-527 | 14 | |
| β-strand | 532-533 | 2 | 2 |
| β-strand | 537-540 | 4 | 2 |
| α-helix | 543-544 | 2 | |
| β-strand | 556-566 | 11 | 2 |
| α-helix | 569-584 | 16 | |
| α-helix | 590-592 | 3 | |
| β-strand | 593-604 | 12 | 2 |
Chain D: 8 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 476-489 | 14 | |
| β-strand | 503-511 | 9 | 2 |
| α-helix | 514-527 | 14 | |
| β-strand | 532-533 | 2 | 2 |
| α-helix | 534-536 | 3 | |
| β-strand | 537-540 | 4 | 2 |
| α-helix | 541 | 1 | |
| α-helix | 543-544 | 2 | |
| α-helix | 549-552 | 4 | |
| β-strand | 556-566 | 11 | 2 |
| α-helix | 569-583 | 15 | |
| α-helix | 590-592 | 3 | |
| β-strand | 593-604 | 12 | 2 |
Chain E: 8 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 478-489 | 12 | |
| β-strand | 503-511 | 9 | 3 |
| α-helix | 514-527 | 14 | |
| β-strand | 532-533 | 2 | 3 |
| α-helix | 534-536 | 3 | |
| β-strand | 537-540 | 4 | 3 |
| α-helix | 541 | 1 | |
| α-helix | 549-552 | 4 | |
| β-strand | 556-566 | 11 | 3 |
| α-helix | 569-583 | 15 | |
| α-helix | 587 | 1 | |
| α-helix | 590-592 | 3 | |
| β-strand | 593-604 | 12 | 3 |
Chain F: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 476-489 | 14 | |
| β-strand | 503-511 | 9 | 3 |
| α-helix | 514-527 | 14 | |
| β-strand | 532-533 | 2 | 3 |
| β-strand | 537-540 | 4 | 3 |
| α-helix | 541 | 1 | |
| α-helix | 543-544 | 2 | |
| β-strand | 556-566 | 11 | 3 |
| α-helix | 569-584 | 16 | |
| α-helix | 587 | 1 | |
| α-helix | 590-592 | 3 | |
| β-strand | 593-604 | 12 | 3 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Epstein-Barr nuclear antigen 1 | A, B, C, D, E, F | protein | 154 | Epstein-Barr virus | P03211 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>5WMF_1 Epstein-Barr nuclear antigen 1 (chains A, B, C, D, E, F)
GSHMGQGGSNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRGTA
LAIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDAIKDLVMT
KPAPTCNIRVTVCSFDDGVDLPPWFPPMVEGAAA
Primary citation
Structural and Functional Basis for an EBNA1 Hexameric Ring in Epstein-Barr Virus Episome Maintenance. Deakyne, J.S., Malecka, K.A., Messick, T.E. et al. J Virol (2017) 91. DOI 10.1128/JVI.01046-17 · PubMed
Other PDB entries of the same protein (UniProt P03211 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6VH6 1.3 Å, Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragment
- 6NPP 1.35 Å, Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments
- 2FYY 1.5 Å, The role of T cell receptor alpha genes in directing human MHC restriction
- 6NPI 1.5 Å, Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments
- 6NPM 1.6 Å, Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragments
- 4PRE 1.65 Å, Crystal structure of a HLA-B*35:08-HPVG-Q5
- 1YY6 1.7 Å, The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with an EBNA1…
- 4PRA 1.85 Å, Crystal structure of a HLA-B*35:01-HPVG-Q5
- 2FZ3 1.9 Å, The role of T cell receptor alpha genes in directing human MHC restriction
- 3MV7 2.0 Å, Crystal Structure of the TK3 TCR in complex with HLA-B*3501/HPVG
- 5WUM 2.0 Å, Crystal structure of mouse importin-alpha1 bound to S385-phosphorylated NLS of EBNA1
- 3MV8 2.1 Å, Crystal Structure of the TK3-Gln55His TCR in complex with HLA-B*3501/HPVG
Browse structure collections
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