3DM1: Chromobox protein homolog 3
Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide. Determined by X-ray diffraction at 2.4 Å resolution. Released 19 Aug 2008.
- Method
- X-ray diffraction
- Resolution
- 2.4 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 2,109
- Mol. weight
- 33.2 kDa
- Released
- 19 Aug 2008
Explore 3DM1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3DM1 contains 11 α-helices and 22 β-strands across 8 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: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30-31 | 2 | 1 |
| β-strand | 32-41 | 10 | 2 |
| β-strand | 44-51 | 8 | 2 |
| α-helix | 56-58 | 3 | |
| β-strand | 60-63 | 4 | 2 |
| α-helix | 64-66 | 3 | |
| β-strand | 67 | 1 | 1 |
| α-helix | 70-78 | 9 | |
Chains B, F and H: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 162-163 | 2 | 1 |
Chain C: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30 | 1 | 3 |
| β-strand | 32-41 | 10 | 4 |
| β-strand | 44-51 | 8 | 4 |
| α-helix | 56-58 | 3 | |
| β-strand | 60-63 | 4 | 4 |
| α-helix | 64-66 | 3 | |
| α-helix | 70-79 | 10 | |
Chain D: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 163 | 1 | 3 |
Chain E: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30-31 | 2 | 5 |
| β-strand | 32-40 | 9 | 6 |
| β-strand | 45-51 | 7 | 6 |
| β-strand | 59-63 | 5 | 6 |
| α-helix | 64-66 | 3 | |
| α-helix | 70-78 | 9 | |
Chain G: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30-31 | 2 | 7 |
| β-strand | 32-40 | 9 | 8 |
| β-strand | 45-51 | 7 | 8 |
| α-helix | 56-58 | 3 | |
| β-strand | 60-63 | 4 | 8 |
| α-helix | 64-66 | 3 | |
| β-strand | 67 | 1 | 7 |
| α-helix | 70-78 | 9 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Chromobox protein homolog 3 | A, C, E, G | protein | 58 | Homo sapiens | Q13185 (AlphaFold model) |
| Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 | B, D, F, H | protein | 12 | | Q96KQ7 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G), FASTA
>3DM1_1 Chromobox protein homolog 3 (chains A, C, E, G)
EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQKAGKEK
Sequence of entity 2 (B, D, F, H), FASTA
>3DM1_2 Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 (chains B, D, F, H)
KVHRARKTMSKP
Primary citation
Structural basis of the chromodomain of Cbx3 bound to methylated peptides from histone h1 and G9a. Ruan, J., Ouyang, H., Amaya, M.F. et al. PLoS One (2012) 7:e35376-e35376. DOI 10.1371/journal.pone.0035376 · PubMed
Other PDB entries of the same protein (UniProt Q13185 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5T1I 1.6 Å, CBX3 chromo shadow domain in complex with histone H3 peptide
- 3KUP 1.77 Å, Crystal Structure of the CBX3 Chromo Shadow Domain
- 9OSC 1.77 Å, Crystal structure of HP1gamma chromoshadow domain in complex with KAP1 peptide
- 8JZW 1.8 Å, Cystal structure of HP1 in complex with TRIM66 peptide
- 3TZD 1.81 Å, Crystal structure of the complex of Human Chromobox Homolog 3 (CBX3)
- 6HW2 1.94 Å, The Crystal Structure of CaV beta4c in complex with HP1gamma chromo shadow domains
- 2L11 Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide
Browse structure collections
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