7VCQ: Viral protein BKRF4
structure of viral protein BKRF4 in complex with H3.3-H4-ASF1. Determined by X-ray diffraction at 3.0 Å resolution. Released 3 Aug 2022.
- Method
- X-ray diffraction
- Resolution
- 3.0 Å
- Organisms
- Homo sapiens, Epstein-Barr virus (strain AG876)
- Chains
- 10
- Atoms
- 7,410
- Mol. weight
- 121.92 kDa
- Released
- 3 Aug 2022
Explore 7VCQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VCQ contains 39 α-helices and 49 β-strands across 10 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-77 | 14 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 85 | 1 | |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 2 |
| α-helix | 121-129 | 9 | |
Chain B: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21-24 | 4 | 3 |
| α-helix | 31-40 | 10 | |
| β-strand | 45-47 | 3 | 2 |
| α-helix | 49-75 | 27 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-91 | 9 | |
| β-strand | 95-97 | 3 | 4 |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-77 | 14 | |
| α-helix | 83 | 1 | |
| β-strand | 84 | 1 | 7 |
| α-helix | 85 | 1 | |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 8 |
| α-helix | 121-130 | 10 | |
Chain D: 6 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-12 | 9 | 5 |
| β-strand | 16-17 | 2 | 4 |
| α-helix | 21 | 1 | |
| β-strand | 22-30 | 9 | 5 |
| β-strand | 34 | 1 | 6 |
| β-strand | 38-45 | 8 | 4 |
| α-helix | 51-53 | 3 | |
| β-strand | 54-62 | 9 | 4 |
| β-strand | 65 | 1 | 6 |
| β-strand | 68-76 | 9 | 5 |
| α-helix | 77-79 | 3 | |
| α-helix | 81-83 | 3 | |
| α-helix | 86-88 | 3 | |
| β-strand | 91-101 | 11 | 4 |
| β-strand | 104-117 | 14 | 4 |
| α-helix | 120-124 | 5 | |
| β-strand | 135-139 | 5 | 4 |
| β-strand | 145-148 | 4 | 4 |
Chain E: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 8 |
| α-helix | 49-74 | 26 | |
| β-strand | 81 | 1 | 7 |
| α-helix | 84-93 | 10 | |
| β-strand | 95-97 | 3 | 9 |
Chain F: 5 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-12 | 9 | 10 |
| β-strand | 16-17 | 2 | 9 |
| α-helix | 21 | 1 | |
| β-strand | 22-30 | 9 | 10 |
| β-strand | 34 | 1 | 11 |
| β-strand | 38-45 | 8 | 9 |
| α-helix | 51-53 | 3 | |
| β-strand | 54-62 | 9 | 9 |
| β-strand | 65 | 1 | 11 |
| β-strand | 68-76 | 9 | 10 |
| α-helix | 77-79 | 3 | |
| α-helix | 81-83 | 3 | |
| β-strand | 91-101 | 11 | 9 |
| β-strand | 104-117 | 14 | 9 |
| α-helix | 120-124 | 5 | |
| β-strand | 135-148 | 14 | 9 |
Chain G: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-76 | 13 | |
| α-helix | 86-107 | 22 | |
| α-helix | 121-129 | 9 | |
Chain H: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| α-helix | 50-76 | 27 | |
| α-helix | 84-91 | 8 | |
| β-strand | 95-98 | 4 | 12 |
2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.3 | A, C, G | protein | 79 | Homo sapiens | P84243 (AlphaFold model) |
| Histone H4 | B, E, H | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone chaperone ASF1B | D, F, I | protein | 156 | Homo sapiens | Q9NVP2 (AlphaFold model) |
| Tegument protein BKRF4 | K | protein | 70 | Epstein-Barr virus (strain AG876) | P30117 (AlphaFold model) |
Sequence of entity 1 (A, C, G), FASTA
>7VCQ_1 Histone H3.3 (chains A, C, G)
STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, E, H), FASTA
>7VCQ_2 Histone H4 (chains B, E, H)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (D, F, I), FASTA
>7VCQ_3 Histone chaperone ASF1B (chains D, F, I)
MAKVSVLNVAVLENPSPFHSPFRFEISFECSEALADDLEWKIIYVGSAESEEFDQILDSV
LVGPVPAGRHMFVFQADAPNPSLIPETDAVGVTVVLITCTYHGQEFIRVGYYVNNEYLNP
ELRENPPMKPDFSQLQRNILASNPRVTRFHINWDNN
Sequence of entity 4 (K), FASTA
>7VCQ_4 Tegument protein BKRF4 (chains K)
GPLGSDTDESDYSDEDEEIDLEEEYPSDEDPSEGSDSDPSWHPSDSDESDYSESDEDEAT
PGSQASRSSR
Primary citation
Epstein-Barr Virus Tegument Protein BKRF4 is a Histone Chaperone. Liu, Y., Li, Y., Bao, H. et al. J Mol Biol (2022) 434:167756-167756. DOI 10.1016/j.jmb.2022.167756 · PubMed
Other PDB entries of the same protein (UniProt P84243 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3QL9 0.93 Å, Monoclinic complex structure of ATRX ADD bound to histone H3K9me3 peptide
- 4GNE 1.47 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7
- 4L58 1.48 Å, Crystal structure of the MLL5 PHD finger in complex with H3K4me3
- 5JLB 1.5 Å, Crystal structure of SETD2 bound to histone H3.3 K36I peptide
- 4GNF 1.55 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15
- 3QLA 1.6 Å, Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide
- 3MUL 1.65 Å, Crystal structure of Brd4 bromodomain 1 with butyrylated histone H3-K(buty)14
- 9G4A 1.65 Å, Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide
- 4GNG 1.73 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide
- 3MUK 1.75 Å, Crystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(prop)23
- 4QQ4 1.75 Å, CW-type zinc finger of MORC3 in complex with the amino terminus of histone H3
- 1PDQ 1.76 Å, Polycomb chromodomain complexed with the histone H3 tail containing trimethyllysine 27.
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