9UX9: Histone H3
local ATPase-NCP structure of the ncBAF-nucleosome complex in the ADP-BeFx-bound state. Determined by electron microscopy at 3.05 Å resolution. Released 18 Mar 2026.
- Method
- Electron microscopy
- Resolution
- 3.05 Å
- Organisms
- Xenopus laevis, artificial sequences, Homo sapiens
- Chains
- 11
- Atoms
- 14,988
- Mol. weight
- 397.08 kDa
- Ligands
- MG, BEF, ADP
- Released
- 18 Mar 2026
Explore 9UX9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9UX9 contains 66 α-helices and 29 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 A: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 2 |
| α-helix | 121-130 | 10 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-27 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 96-97 | 2 | 3 |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-72 | 27 | |
| α-helix | 80-88 | 9 | |
| α-helix | 92-96 | 5 | |
| β-strand | 100-102 | 3 | 5 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 103-118 | 16 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 6 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 7 |
| α-helix | 121-131 | 11 | |
Chain F: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-38 | 8 | |
| β-strand | 45-46 | 2 | 7 |
| α-helix | 50-73 | 24 | |
| β-strand | 80-81 | 2 | 6 |
| α-helix | 83-93 | 11 | |
| β-strand | 96-98 | 3 | 5 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-35 | 8 | |
| β-strand | 42-43 | 2 | 8 |
| α-helix | 46-72 | 27 | |
| β-strand | 77 | 1 | 9 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-101 | 2 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50 | 1 | 9 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 8 |
| α-helix | 88-98 | 11 | |
| α-helix | 103-119 | 17 | |
1 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 | A, E | protein | 135 | Xenopus laevis | A0A310TTQ1 (AlphaFold model) |
| Histone H4 | B, F | protein | 102 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 131 | Xenopus laevis | Q6AZJ8 (AlphaFold model) |
| Histone H2B | D, H | protein | 122 | Xenopus laevis | A0A8J0U496 (AlphaFold model) |
| DNA (167-mer) | I | DNA | 167 | artificial sequences | |
| DNA (167-mer) | J | DNA | 167 | artificial sequences | |
| SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 | K | protein | 1648 | Homo sapiens | P51532 |
Sequence of entity 1 (A, E), FASTA
>9UX9_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9UX9_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9UX9_3 Histone H2A (chains C, G)
NASGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYL
TAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK
KTESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>9UX9_4 Histone H2B (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK
Sequence of entity 5 (I), FASTA
>9UX9_5 DNA (167-MER) (chains I)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGTTCTAGAGCGGCCGCCACCGC
Sequence of entity 6 (J), FASTA
>9UX9_6 DNA (167-MER) (chains J)
GCGGTGGCGGCCGCTCTAGAACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
Sequence of entity 7 (K), FASTA
>9UX9_7 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 (chains K)
MASTPDPPLGGTPRPGPSPGPGPSPGAMLGPSPGPSPGSAHSMMGPSPGPPSAGHPIPTQ
GPGGYPQDNMHQMHKPMESMHEKGMSDDPRYNQMKGMGMRSGGHAGMGPPPSPMDQHSQG
YPSPLGGSEHASSPVPASGPSSGPQMSSGPGGAPLDGADPQALGQQNRGPTPFNQNQLHQ
LRAQIMAYKMLARGQPLPDHLQMAVQGKRPMPGMQQQMPTLPPPSVSATGPGPGPGPGPG
PGPGPAPPNYSRPHGMGGPNMPPPGPSGVPPGMPGQPPGGPPKPWPEGPMANAAAPTSTP
QKLIPPQPTGRPSPAPPAVPPAASPVMPPQTQSPGQPAQPAPMVPLHQKQSRITPIQKPR
GLDPVEILQEREYRLQARIAHRIQELENLPGSLAGDLRTKATIELKALRLLNFQRQLRQE
VVVCMRRDTALETALNAKAYKRSKRQSLREARITEKLEKQQKIEQERKRRQKHQEYLNSI
LQHAKDFKEYHRSVTGKIQKLTKAVATYHANTEREQKKENERIEKERMRRLMAEDEEGYR
KLIDQKKDKRLAYLLQQTDEYVANLTELVPQHKAAQVAKEKKKKKKKKKAENAEGQTPAI
GPDGEPLDETSQMSDLPVKVIHVESGKILTGTDAPKAGQLEAWLEMNPGYEVAPRSDSEE
SGSEEEEEEEEEEQPQAAQPPTLPVEEKKKIPDPDSDDVSEVDARHIIENAKQDVDDEYG
VSQALARGLQSYYAVAHAVTERVDKQSALMVNGVLKQYQIKGLEWLVSLYNNNLNGILAD
EMGLGKTIQTIALITYLMEHKRINGPFLIIVPLSTLSNWAYEFDKWAPSVVKVSYKGSPA
ARRAFVPQLRSGKFNVLLTTYEYIIKDKHILAKIRWKYMIVDEGHRMKNHHCKLTQVLNT
HYVAPRRLLLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFNAPFAMTGEKVDLNEE
ETILIIRRLHKVLRPFLLRRLKKEVEAQLPEKVEYVIKCDMSALQRVLYRHMQAKGVLLT
DGSEKDKKGKGGTKTLMNTIMQLRKICNHPYMFQHIEESFSEHLGFTGGIVQGLDLYRAS
GKFELLDRILPKLRATNHKVLLFCQMTSLMTIMEDYFAYRGFKYLRLDGTTKAEDRGMLL
KTFNEPGSEYFIFLLSTRAGGLGLNLQSADTVIIFDSDWNPHQDLQAQDRAHRIGQQNEV
RVLRLCTVNSVEEKILAAAKYKLNVDQKVIQAGMFDQKSSSHERRAFLQAILEHEEQDES
RHCSTGSGSASFAHTAPPPAGVNPDLEEPPLKEEDEVPDDETVNQMIARHEEEFDLFMRM
DLDRRREEARNPKRKPRLMEEDELPSWIIKDDAEVERLTCEEEEEKMFGRGSRHRKEVDY
SDSLTEKQWLKAIEEGTLEEIEEEVRQKKSSRKRKRDSDAGSSTPTTSTRSRDKDDESKK
QKKRGRPPAEKLSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYE
LIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTS
VRQKIEKEDDSEGEESEEEEEGEEEGSESESRSVKVKIKLGRKEKAQDRLKGGRRRPSRG
SRAKPVVSDDDSEEEQEEDRSGSGSEED
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1 |
| BEF | Beryllium trifluoride ion | Be F3 | 1 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
Primary citation
Structural basis for BCL7B-mediated ncBAF-nucleosome engagement. Sun, F., Zou, B., Li, H. et al. Nucleic Acids Res (2026) 54. DOI 10.1093/nar/gkag092 · PubMed
Other PDB entries of the same protein (UniProt A0A310TTQ1 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
- 9JNP 2.3 Å, Structure of isw1-nucleosome complex in ATP state
- 8RUP 2.42 Å, Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
- 9JNU 2.5 Å, Structure of isw1-nucleosome complex in ADP state
- 9N6H 2.54 Å, 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex
- 9N6I 2.61 Å, 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex
- 9JNT 2.7 Å, Structure of isw1-nucleosome complex in ADP* state
- 9LIU 2.7 Å, Structure of isw1-nucleosome double-bound complex in ATP-ATP state
- 28OE 2.74 Å, Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
- 9JO5 2.8 Å, Structure of isw1-nucleosome complex in ADP-B state
- 9V9Q 2.8 Å, Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified…
- 9C9X 2.83 Å, S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome
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