8Q3E: PDB entry 8Q3E
High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide. Determined by X-ray diffraction at 2.17 Å resolution. Released 27 Mar 2024.
- Method
- X-ray diffraction
- Resolution
- 2.17 Å
- Organisms
- Human spumaretrovirus, Homo sapiens
- Chains
- 11
- Atoms
- 12,197
- Mol. weight
- 179.3 kDa
- Ligands
- MG
- Released
- 27 Mar 2024
Explore 8Q3E in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8Q3E contains 39 α-helices and 20 β-strands across 9 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 AAA: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chain BBB: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain CCC: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 6 |
| α-helix | 113-115 | 3 | |
Chains DDD and HHH: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-119 | 19 | |
Chain EEE: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-42 | 3 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-131 | 11 | |
Chain FFF: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 6 |
Chain GGG: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 113-115 | 3 | |
Chain MMM: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 544-546 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Gly-gly-tyr-asn-leu-arg-pro-arg-thr-tyr-gln-pro-gln-arg-tyr-gly-gly-gly | MMM | protein | 18 | Human spumaretrovirus | P14349 |
| Histone H3.1 | AAA, EEE | protein | 98 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | BBB, FFF | protein | 87 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | CCC, GGG | protein | 107 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-K | DDD, HHH | protein | 95 | Homo sapiens | O60814 |
| DNA (145-mer) | III | DNA | 145 | Homo sapiens | |
| DNA (145-mer) | JJJ | DNA | 145 | Homo sapiens | |
Sequence of entity 1 (MMM), FASTA
>8Q3E_1 GLY-GLY-TYR-ASN-LEU-ARG-PRO-ARG-THR-TYR-GLN-PRO-GLN-ARG-TYR-GLY-GLY-GLY (chains MMM)
GGYNLRPRTYQPQRYGGG
Sequence of entity 2 (AAA, EEE), FASTA
>8Q3E_2 Histone H3.1 (chains AAA, EEE)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACE
AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sequence of entity 3 (BBB, FFF), FASTA
>8Q3E_3 Histone H4 (chains BBB, FFF)
KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH
AKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 4 (CCC, GGG), FASTA
>8Q3E_4 Histone H2A type 1-B/E (chains CCC, GGG)
KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARD
NKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
Sequence of entity 5 (DDD, HHH), FASTA
>8Q3E_5 Histone H2B type 1-K (chains DDD, HHH)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Sequence of entity 6 (III), FASTA
>8Q3E_6 DNA (145-MER) (chains III)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTG
GTAGTATCTGCAGGTGGATATTGAT
Sequence of entity 7 (JJJ), FASTA
>8Q3E_7 DNA (145-MER) (chains JJJ)
ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTG
GTAGTATCTGCAGGTGGATATTGAT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1 |
Primary citation
Viral peptide conjugates for metal-warhead delivery to chromatin. Batchelor, L.K., De Falco, L., Dyson, P.J. et al. RSC Adv (2024) 14:8718-8725. DOI 10.1039/d4ra01617c · PubMed
Other PDB entries of the same protein (UniProt P14349), best resolution first:
- 4JNH 2.4 Å, A unique spumavirus gag N-terminal domain with functional properties of orthoretroviral…
- 8Q36 2.6 Å, Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG…
- 5MLU 2.8 Å, Crystal structure of the PFV GAG CBS bound to a mononucleosome
- 4JMR 2.9 Å, A unique spumavirus gag N-terminal domain with functional properties of orthoretroviral…
- 5M1G Structure of a Spumaretrovirus Gag central domain reveals an ancient retroviral capsid
- 5M1H Structure of a Spumaretrovirus Gag central domain reveals an ancient retroviral capsid
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