8UXQ: Heterochromatin Protein 1 (HP1) alpha
Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome. Determined by electron microscopy at 6.3 Å resolution. Released 25 Sept 2024.
- Method
- Electron microscopy
- Resolution
- 6.3 Å
- Organisms
- Homo sapiens, Xenopus laevis, Mus musculus
- Chains
- 12
- Atoms
- 12,603
- Mol. weight
- 281.48 kDa
- Released
- 25 Sept 2024
Explore 8UXQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8UXQ contains 44 α-helices and 26 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: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-10 | 2 | 1 |
| β-strand | 13-14 | 2 | 1 |
| α-helix | 18-20 | 3 | |
| α-helix | 25-27 | 3 | |
| α-helix | 39-53 | 15 | |
| β-strand | 119 | 1 | 2 |
| β-strand | 128 | 1 | 2 |
| α-helix | 135-138 | 4 | |
| α-helix | 140-146 | 7 | |
| α-helix | 157-164 | 8 | |
| α-helix | 166-169 | 4 | |
Chain C: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 177-180 | 4 | 3 |
| β-strand | 183-187 | 5 | 3 |
| β-strand | 200-201 | 2 | 3 |
| α-helix | 210-224 | 15 | |
| β-strand | 272-276 | 5 | 4 |
| β-strand | 288-291 | 4 | 4 |
| β-strand | 297-299 | 3 | 4 |
| α-helix | 310-317 | 8 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 334-341 | 8 | |
| α-helix | 353-363 | 11 | |
| β-strand | 371-372 | 2 | 5 |
| α-helix | 376-401 | 26 | |
| β-strand | 406 | 1 | 6 |
| α-helix | 411-419 | 9 | |
Chain F: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 438-444 | 7 | |
| β-strand | 452 | 1 | 6 |
| α-helix | 457-482 | 26 | |
| β-strand | 487-488 | 2 | 5 |
| α-helix | 492-498 | 7 | |
Chain G: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 513-517 | 5 | |
| α-helix | 524-533 | 10 | |
| α-helix | 546-564 | 19 | |
| β-strand | 574 | 1 | 7 |
| α-helix | 575-576 | 2 | |
| α-helix | 577-585 | 9 | |
| α-helix | 590-593 | 4 | |
| β-strand | 597 | 1 | 8 |
| α-helix | 604-606 | 3 | |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 625-634 | 10 | |
| β-strand | 639 | 1 | 7 |
| α-helix | 644-665 | 22 | |
| α-helix | 678-687 | 10 | |
| α-helix | 694-707 | 14 | |
Chain K: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 715-724 | 10 | |
| α-helix | 734-747 | 14 | |
| β-strand | 753 | 1 | 9 |
| α-helix | 756-778 | 23 | |
| β-strand | 787 | 1 | 10 |
| α-helix | 790-800 | 11 | |
Chain L: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 807-809 | 3 | |
| α-helix | 813-820 | 8 | |
| β-strand | 827 | 1 | 10 |
| α-helix | 832-857 | 26 | |
| β-strand | 863 | 1 | 9 |
| α-helix | 865-874 | 10 | |
| β-strand | 879 | 1 | 8 |
| β-strand | 881 | 1 | 11 |
| β-strand | 883 | 1 | 11 |
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 |
|---|
| Chromobox protein homolog 5 | A, C | protein | 195 | Homo sapiens | P45973 (AlphaFold model) |
| Histone H3.2 | E, K | protein | 135 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | F, L | protein | 102 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A.Z | G, M | protein | 127 | Mus musculus | P0C0S6 (AlphaFold model) |
| Histone H2B 1.1 | H, N | protein | 125 | Xenopus laevis | P02281 |
| DNA Widom601 (208bp) strand1 | I | DNA | 208 | synthetic construct | |
| DNA Widom601 (208bp) strand2 | J | DNA | 208 | synthetic construct | |
Sequence of entity 1 (A, C), FASTA
>8UXQ_1 Chromobox protein homolog 5 (chains A, C)
GSPEFGKKTKRTADSSSSEDEEEYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKN
LDCPELISEFMKKYKKMKEGENNKPREKSESNKRKSNFSNSADDIKSKKKREQSNDIARG
FERGLEPEKIIGATDSCGDLMFLMKWKDTDEADLVLAKEANVKCPQIVIAFYEERLTWHA
YPEDAENKEKETAKS
Sequence of entity 2 (E, K), FASTA
>8UXQ_2 Histone H3.2 (chains E, K)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 3 (F, L), FASTA
>8UXQ_3 Histone H4 (chains F, L)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 4 (G, M), FASTA
>8UXQ_4 Histone H2A.Z (chains G, M)
AGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEY
LTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGK
KGQQKTV
Sequence of entity 5 (H, N), FASTA
>8UXQ_5 Histone H2B 1.1 (chains H, N)
PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMS
IMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK
Sequence of entity 6 (I), FASTA
>8UXQ_6 DNA Widom601 (208bp) strand1 (chains I)
ACTCCGGCAAGGTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGG
AGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTA
AGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGC
GGCCGCGTATAGGGTCCATCACATAAGT
Sequence of entity 7 (J), FASTA
>8UXQ_7 DNA Widom601 (208bp) strand2 (chains J)
ACTTATGTGATGGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCA
ATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTT
AACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGC
ATGTATTGAACAGCGACCTTGCCGGAGT
Primary citation
Structural mechanism of HP1⍺-dependent transcriptional repression and chromatin compaction. Sokolova, V., Miratsky, J., Svetlov, V. et al. Structure (2024) 32:2094-2106.e6. DOI 10.1016/j.str.2024.09.013 · 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
- 9CMT 3.17 Å, The crystal structure of HP1alpha CSD-Agno complex
Browse structure collections
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