8QZ0: SWR1-hexasome-dimer complex
SWR1-hexasome-dimer complex. Determined by electron microscopy at 3.8 Å resolution. Released 2 Oct 2024.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organisms
- Saccharomyces cerevisiae S288C, synthetic construct
- Chains
- 22
- Atoms
- 44,167
- Mol. weight
- 893.3 kDa
- Ligands
- ADP, BEF, MG, ZN
- Released
- 2 Oct 2024
Explore 8QZ0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8QZ0 contains 245 α-helices and 207 β-strands across 20 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, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 43-53 | 11 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 90-113 | 24 | |
| α-helix | 121-129 | 9 | |
Chain B: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-55 | 11 | |
| α-helix | 64-73 | 10 | |
| α-helix | 86-97 | 12 | |
| α-helix | 100-113 | 14 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-130 | 10 | |
Chain C: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 51-73 | 23 | |
| α-helix | 83-93 | 11 | |
| β-strand | 97 | 1 | 3 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| α-helix | 48-74 | 27 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-93 | 11 | |
Chain E: 6 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 29-38 | 10 | |
| α-helix | 51-73 | 23 | |
| α-helix | 81-89 | 9 | |
| α-helix | 92-97 | 6 | |
| β-strand | 102 | 1 | 3 |
| α-helix | 108-110 | 3 | |
Chain G: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| α-helix | 61-86 | 26 | |
| α-helix | 94-104 | 11 | |
| α-helix | 107-125 | 19 | |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56-57 | 2 | 4 |
| α-helix | 59-86 | 28 | |
| α-helix | 94-104 | 11 | |
| α-helix | 107-124 | 18 | |
Chain K: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 67-77 | 11 | |
| α-helix | 81-83 | 3 | |
| α-helix | 89-92 | 4 | |
| α-helix | 117-121 | 5 | |
| α-helix | 141-147 | 7 | |
| α-helix | 149-151 | 3 | |
12 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, B | protein | 136 | Saccharomyces cerevisiae S288C | P61830 (AlphaFold model) |
| Histone H4 | C, D | protein | 103 | Saccharomyces cerevisiae S288C | P02309 (AlphaFold model) |
| Histone H2A.1 | E | protein | 132 | Saccharomyces cerevisiae S288C | P04911 (AlphaFold model) |
| Histone H2B.1 | G | protein | 131 | Saccharomyces cerevisiae S288C | P02293 (AlphaFold model) |
| Histone H2B.1 | H | protein | 131 | Saccharomyces cerevisiae S288C | P02293 (AlphaFold model) |
| DNA (113-mer) | I | DNA | 118 | synthetic construct | |
| DNA (113-mer) | J | DNA | 118 | synthetic construct | |
| Histone H2A.Z | L | protein | 134 | Saccharomyces cerevisiae S288C | Q12692 |
| SWR1-complex protein 5 | P | protein | 303 | Saccharomyces cerevisiae S288C | P38326 |
| Actin-like protein ARP6 | R | protein | 438 | Saccharomyces cerevisiae S288C | Q12509 |
| Vacuolar protein sorting-associated protein 71 | S | protein | 280 | Saccharomyces cerevisiae S288C | Q03433 |
| RuvB-like protein 2 | U, W, Y | protein | 471 | Saccharomyces cerevisiae S288C | Q12464 |
4 more molecules are not listed.
Sequence of entity 1 (A, B), FASTA
>8QZ0_1 Histone H3 (chains A, B)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
MPKEIQLARRLRGERS
Sequence of entity 2 (C, D), FASTA
>8QZ0_2 Histone H4 (chains C, D)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
Sequence of entity 3 (E), FASTA
>8QZ0_3 Histone H2A.1 (chains E)
MSGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKATKASQEL
Sequence of entity 4 (G), FASTA
>8QZ0_4 Histone H2B.1 (chains G)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Sequence of entity 5 (H), FASTA
>8QZ0_5 Histone H2B.1 (chains H)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVCEGTR
AVTKYSSSTQA
Sequence of entity 6 (I), FASTA
>8QZ0_6 DNA (113-MER) (chains I)
CCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTT
AAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTC
Sequence of entity 7 (J), FASTA
>8QZ0_7 DNA (113-MER) (chains J)
GACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAA
GCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGG
Sequence of entity 8 (L), FASTA
>8QZ0_8 Histone H2A.Z (chains L)
MSGKAHGGKGKSGAKDSGSLRSQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYL
TAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGDDELDSLIRATIASGGVLPHIN
KALLLKVEKKGSKK
Sequence of entity 9 (P), FASTA
>8QZ0_9 SWR1-complex protein 5 (chains P)
MPEVETKIIPNEKEDEDEDGYIEEEDEDFQPEKDKLGGGSDDSDASDGGDDYDDGVNRDK
GRNKVDYSRIESESGGLIKTRRARQAEEEYAKTHKYESLTVESIPAKVNSIWEELQEASK
NRLLSSSGKVGSVLDGSKEARSTTAAQQEDKILIERNYKFAGETVHEKKWVSRSSAEGQE
YLNSLKFKQQAPAAPVQLEKAVRTKSNESRQHLRRPLKRPPLLEQIISGGLRPKLTTLEK
SQLDWASYVDRAGLNDELVLHNKDGFLARQEFLQRVGSAEDERYKELRRQQLAQQLQQDS
EAS
Sequence of entity 10 (R), FASTA
>8QZ0_10 Actin-like protein ARP6 (chains R)
METPPIVIDNGSYEIKFGPSTNKKPFRALNALAKDKFGTSYLSNHIKNIKDISSITFRRP
HELGQLTLWELESCIWDYCLFNPSEFDGFDLKEGKGHHLVASESCMTLPELSKHADQVIF
EEYEFDSLFKSPVAVFVPFTKSYKGEMRTISGKDEDIDIVRGNSDSTNSTSSESKNAQDS
GSDYHDFQLVIDSGFNCTWIIPVLKGIPYYKAVKKLDIGGRFLTGLLKETLSFRHYNMMD
ETILVNNIKEQCLFVSPVSYFDSFKTKDKHALEYVLPDFQTSFLGYVRNPRKENVPLPED
AQIITLTDELFTIPETFFHPEISQITKPGIVEAILESLSMLPEIVRPLMVGNIVCTGGNF
NLPNFAQRLAAELQRQLPTDWTCHVSVPEGDCALFGWEVMSQFAKTDSYRKARVTREEYY
EHGPDWCTKHRFGYQNWI
Sequence of entity 11 (S), FASTA
>8QZ0_11 Vacuolar protein sorting-associated protein 71 (chains S)
MKALVEEIDKKTYNPDIYFTSLDPQARRYTSKKINKQGTISTSRPVKRINYSLADLEARL
YTSRSEGDGNSISRQDDRNSKNSHSFEERYTQQEILQSDRRFMELNTENFSDLPNVPTLL
SDLTGVPRDRIESTTKPISQTSDGLSALMGGSSFVKEHSKYGHGWVLKPETLREIQLSYK
STKLPKPKRKNTNRIVALKKVLSSKRNLHSFLDSALLNLMDKNVIYHNVYNKRYFKVLPL
ITTCSICGGYDSISSCVNCGNKICSVSCFKLHNETRCRNR
Sequence of entity 12 (U, W, Y), FASTA
>8QZ0_12 RuvB-like protein 2 (chains U, W, Y)
MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKM
VQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQA
FRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLT
KEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS
LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHM
LDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYN
EQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEV
EDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAKSADPDAMDTTE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 8 |
| BEF | Beryllium trifluoride ion | Be F3 | 2 |
| MG | Magnesium ion | Mg | 8 |
| ZN | Zinc ion | Zn | 2 |
Primary citation
Stabilization of the hexasome intermediate during histone exchange by yeast SWR1 complex. Jalal, A.S.B., Girvan, P., Chua, E.Y.D. et al. Mol Cell (2024) 84:3871. DOI 10.1016/j.molcel.2024.08.015 · PubMed
Other PDB entries of the same protein (UniProt P61830 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6KMJ 1.4 Å, Crystal structure of Sth1 bromodomain in complex with H3K14Ac
- 7F3S 1.4 Å, Crystal structure of Sth1 Bromodomain in complex with H3K14bz peptide
- 3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
- 8I3F 1.62 Å, Crystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal
- 2H2G 1.63 Å, The Structural Basis of Sirtuin substrate affinity
- 7F4E 1.78 Å, Crystal structure of Hst2 in complex with H3K9bz peptide
- 5D7E 1.9 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9ac
- 7F4A 2.0 Å, Crystal structure of Taf14 YEATS domain in complex with H3K9bz peptide
- 1M1D 2.2 Å, Tetrahymena GCN5 with bound bisubstrate analog inhibitor
- 1QSN 2.2 Å, Crystal structure of tetrahymena GCN5 with bound coenzyme a and histone H3 peptide
- 2IDC 2.2 Å, Structure of the Histone H3-Asf1 Chaperone Interaction
- 5IOK 2.22 Å, Crystal structure of Taf14 YEATS domain in complex with histone H3K9cr
Browse structure collections
About this viewer
MolViewer shows 8QZ0 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.