9CMT: HP1alpha CSD-Agno complex
The crystal structure of HP1alpha CSD-Agno complex. Determined by X-ray diffraction at 3.17 Å resolution. Released 28 May 2025.
- Method
- X-ray diffraction
- Resolution
- 3.17 Å
- Organisms
- Homo sapiens, JC polyomavirus
- Chains
- 6
- Atoms
- 2,369
- Mol. weight
- 34.05 kDa
- Ligands
- F6Z
- Released
- 28 May 2025
Explore 9CMT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9CMT contains 15 α-helices and 18 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: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 116-119 | 4 | |
| α-helix | 121-122 | 2 | |
| β-strand | 123-130 | 8 | 1 |
| β-strand | 137-142 | 6 | 1 |
| β-strand | 149-152 | 4 | 1 |
| α-helix | 153-159 | 7 | |
| α-helix | 161-170 | 10 | |
| β-strand | 172-175 | 4 | 2 |
Chain B: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 116-119 | 4 | |
| α-helix | 121-122 | 2 | |
| β-strand | 123-130 | 8 | 3 |
| β-strand | 137-142 | 6 | 3 |
| β-strand | 149-152 | 4 | 3 |
| α-helix | 153-159 | 7 | |
| α-helix | 161-170 | 10 | |
| β-strand | 172-173 | 2 | 2 |
Chains C and F: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-13 | 5 | 2 |
Chain D: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 117-119 | 3 | |
| α-helix | 121-122 | 2 | |
| β-strand | 123-130 | 8 | 4 |
| β-strand | 137-142 | 6 | 4 |
| β-strand | 149-152 | 4 | 4 |
| α-helix | 153-159 | 7 | |
| α-helix | 161-169 | 9 | |
| β-strand | 172-175 | 4 | 5 |
Chain E: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 121-122 | 2 | |
| β-strand | 123-130 | 8 | 6 |
| β-strand | 137-142 | 6 | 6 |
| β-strand | 149-152 | 4 | 6 |
| α-helix | 153-159 | 7 | |
| α-helix | 161-169 | 9 | |
| β-strand | 172-173 | 2 | 5 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Chromobox protein homolog 5 | A, B, D, E | protein | 65 | Homo sapiens | P45973 (AlphaFold model) |
| Agnoprotein | C, F | protein | 16 | JC polyomavirus | P03086 (AlphaFold model) |
Sequence of entity 1 (A, B, D, E), FASTA
>9CMT_1 Chromobox protein homolog 5 (chains A, B, D, E)
EIARGFERGLEPEKIIGATDSSGDLMFLMKWKDSDEADLVLAKEANVKCPQIVIAFYEER
LTWHA
Sequence of entity 2 (C, F), FASTA
>9CMT_2 Agnoprotein (chains C, F)
RQLSRKASVKVSKTWS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| F6Z | 3',6'-dihydroxy-3-oxo-3H-SPIRO[2-benzofuran-1,9'-xanthene]-5-carboxylic acid | C21 H12 O7 | 2 |
Primary citation
Chromatin mimicry by human JC virus. Schaefer, U., Miroshnikova, Y.A., Xie, W. et al. bioRxiv (2024). DOI 10.1101/2024.11.04.621823 · PubMed
Other PDB entries of the same protein (UniProt P45973 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3FDT 2.0 Å, Crystal structure of the complex of human chromobox homolog 5 (CBX5) with H3K9(me)3…
- 9CEA 2.15 Å, Crystal structure of HP1alpha chromoshadow domain
- 9CDW 2.4 Å, Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide
- 3I3C 2.48 Å, Crystal Structural of CBX5 Chromo Shadow Domain
- 8UXQ 6.3 Å, Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome
Browse structure collections
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