9NY4: USP21
USP21 bound to H2AK119ub nucleosome. Determined by electron microscopy at 2.98 Å resolution. Released 24 Sept 2025.
- Method
- Electron microscopy
- Resolution
- 2.98 Å
- Organisms
- Xenopus laevis, synthetic construct, Homo sapiens
- Chains
- 12
- Atoms
- 14,936
- Mol. weight
- 249.38 kDa
- Released
- 24 Sept 2025
Explore 9NY4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9NY4 contains 55 α-helices and 43 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: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 47-53 | 7 | |
| α-helix | 64-75 | 12 | |
| β-strand | 84 | 1 | 1 |
| α-helix | 88-112 | 25 | |
| β-strand | 119 | 1 | 2 |
| α-helix | 121-130 | 10 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-39 | 9 | |
| β-strand | 46 | 1 | 2 |
| α-helix | 50-74 | 25 | |
| β-strand | 81 | 1 | 1 |
| α-helix | 83-91 | 9 | |
| β-strand | 96 | 1 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-37 | 11 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 49-72 | 24 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-87 | 8 | |
| α-helix | 93-96 | 4 | |
| β-strand | 100 | 1 | 6 |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 5 |
| α-helix | 53-60 | 8 | |
| α-helix | 62-79 | 18 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 104-119 | 16 | |
Chain E: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-42 | 3 | |
| α-helix | 45-49 | 5 | |
| α-helix | 53-56 | 4 | |
| α-helix | 66-75 | 10 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 88-112 | 25 | |
| β-strand | 119 | 1 | 8 |
| α-helix | 123-131 | 9 | |
Chain F: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-39 | 9 | |
| β-strand | 46 | 1 | 8 |
| α-helix | 50-74 | 25 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-87 | 5 | |
| α-helix | 89-92 | 4 | |
| β-strand | 96 | 1 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-37 | 11 | |
| β-strand | 43 | 1 | 9 |
| α-helix | 49-72 | 24 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 81-87 | 7 | |
| α-helix | 93-96 | 4 | |
| β-strand | 100 | 1 | 3 |
| α-helix | 113-115 | 3 | |
Chain H: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-30 | 4 | |
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 10 |
| α-helix | 53-79 | 27 | |
| β-strand | 86 | 1 | 9 |
| α-helix | 88-98 | 11 | |
| α-helix | 103-118 | 16 | |
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 H3.2 | A, E | protein | 136 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A type 1 | C, G | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D, H | protein | 123 | Xenopus laevis | P02281 (AlphaFold model) |
| 601 DNA (145-mer) | I | DNA | 145 | synthetic construct | |
| 601 DNA (145-mer) | J | DNA | 145 | synthetic construct | |
| Ubiquitin carboxyl-terminal hydrolase 21 | K | protein | 370 | Homo sapiens | Q9UK80 |
| Ubiquitin | U | protein | 80 | Homo sapiens | J3QS39 |
Sequence of entity 1 (A, E), FASTA
>9NY4_1 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9NY4_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9NY4_3 Histone H2A type 1 (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKC
TESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>9NY4_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYT
SAK
Sequence of entity 5 (I), FASTA
>9NY4_5 601 DNA (145-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT
Sequence of entity 6 (J), FASTA
>9NY4_6 601 DNA (145-MER) (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT
Sequence of entity 7 (K), FASTA
>9NY4_7 Ubiquitin carboxyl-terminal hydrolase 21 (chains K)
SDDKMAHHTLLLGSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRA
QELTEAFADVIGALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHL
EINRRGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFV
GQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAP
VCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDFASD
KAGSPVYQLYALCNHSGSVHYGHYTALCRCQTGWHVYNDSRVSPVSENQVASSEGYVLFY
QLMQEPPRCL
Sequence of entity 8 (U), FASTA
>9NY4_8 Ubiquitin (chains U)
GSHMMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGC
Primary citation
Mechanism of USP21 autoinhibition and histone H2AK119 deubiquitination. Rahman, S., Hicks, C.W., Gwizdala, A. et al. Sci Adv (2025) 11:eady2604-eady2604. DOI 10.1126/sciadv.ady2604 · PubMed
Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
- 3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
- 1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
- 1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
- 4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
- 1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
- 3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
- 3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
- 3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
- 3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
- 6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
- 8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
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