8QYV: SWR1-hexasome complex
SWR1-hexasome complex. Determined by electron microscopy at 3.5 Å resolution. Released 2 Oct 2024.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organisms
- Saccharomyces cerevisiae S288C, synthetic construct
- Chains
- 19
- Atoms
- 41,998
- Mol. weight
- 847.19 kDa
- Ligands
- ZN, MG, BEF, ADP
- Released
- 2 Oct 2024
Explore 8QYV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8QYV contains 226 α-helices and 198 β-strands across 17 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, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 48-51 | 4 | |
| α-helix | 64-78 | 15 | |
| α-helix | 89-113 | 25 | |
| α-helix | 121-131 | 11 | |
Chain B: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-42 | 3 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 1 |
| α-helix | 121-130 | 10 | |
Chain C: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13 | 1 | 2 |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 1 |
| α-helix | 50-75 | 26 | |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain D: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| α-helix | 50-74 | 25 | |
| α-helix | 83-90 | 8 | |
| α-helix | 91-93 | 3 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 28-38 | 11 | |
| α-helix | 51-73 | 23 | |
| β-strand | 78 | 1 | 4 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 101-103 | 3 | 3 |
Chain G: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56 | 1 | 4 |
| α-helix | 59-86 | 28 | |
| α-helix | 95-104 | 10 | |
| α-helix | 107-125 | 19 | |
Chain M: 35 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 700-712 | 13 | |
| β-strand | 717-718 | 2 | 5 |
| α-helix | 727-741 | 15 | |
| β-strand | 748-752 | 5 | 5 |
| α-helix | 757-766 | 10 | |
| β-strand | 773-776 | 4 | 5 |
| α-helix | 780-786 | 7 | |
| β-strand | 798-802 | 5 | 5 |
| α-helix | 803-806 | 4 | |
| α-helix | 810-813 | 4 | |
| β-strand | 818-824 | 7 | 5 |
| α-helix | 826-828 | 3 | |
| α-helix | 835-841 | 7 | |
| β-strand | 845-851 | 7 | 5 |
| α-helix | 861-870 | 10 | |
| α-helix | 889-892 | 4 | |
| α-helix | 896-903 | 8 | |
| α-helix | 908-910 | 3 | |
| α-helix | 914-925 | 12 | |
| α-helix | 926-928 | 3 | |
| β-strand | 944-951 | 8 | 6 |
| α-helix | 955-972 | 18 | |
| β-strand | 975 | 1 | 2 |
| α-helix | 982-993 | 12 | |
| β-strand | 1005 | 1 | 7 |
| β-strand | 1008 | 1 | 8 |
| α-helix | 1015-1029 | 15 | |
| α-helix | 1047-1049 | 3 | |
| α-helix | 1056-1064 | 9 | |
| α-helix | 1071-1088 | 18 | |
| α-helix | 1096-1100 | 5 | |
| α-helix | 1105-1132 | 28 | |
| α-helix | 1141-1147 | 7 | |
| α-helix | 1166-1172 | 7 | |
| α-helix | 1174-1179 | 6 | |
| β-strand | 1187 | 1 | 8 |
| α-helix | 1193-1196 | 4 | |
| α-helix | 1209-1219 | 11 | |
| α-helix | 1225-1230 | 6 | |
| β-strand | 1234 | 1 | 7 |
| α-helix | 1240-1243 | 4 | |
| α-helix | 1246-1260 | 15 | |
| β-strand | 1265-1269 | 5 | 6 |
| α-helix | 1272-1284 | 13 | |
| β-strand | 1289-1292 | 4 | 6 |
| α-helix | 1298-1309 | 12 | |
| β-strand | 1316-1320 | 5 | 6 |
| β-strand | 1335-1338 | 4 | 6 |
| α-helix | 1345-1352 | 8 | |
| α-helix | 1363 | 1 | |
| β-strand | 1364-1371 | 8 | 6 |
| α-helix | 1375-1391 | 17 | |
Chain P: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 197-203 | 7 | |
| α-helix | 223-226 | 4 | |
| α-helix | 238-252 | 15 | |
| α-helix | 255-264 | 10 | |
| α-helix | 267-302 | 36 | |
9 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) |
| DNA (118-mer) | I | DNA | 118 | synthetic construct | |
| DNA (118-mer) | J | DNA | 118 | synthetic construct | |
| Helicase SWR1 | M | protein | 1514 | Saccharomyces cerevisiae S288C | Q05471 |
| 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 1 | T, V, X | protein | 463 | Saccharomyces cerevisiae S288C | Q03940 |
| RuvB-like protein 2 | U, W, Y | protein | 471 | Saccharomyces cerevisiae S288C | Q12464 |
1 more molecules are not listed.
Sequence of entity 1 (A, B), FASTA
>8QYV_1 Histone H3 (chains A, B)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
MPKEIQLARRLRGERS
Sequence of entity 2 (C, D), FASTA
>8QYV_2 Histone H4 (chains C, D)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
Sequence of entity 3 (E), FASTA
>8QYV_3 Histone H2A.1 (chains E)
MSGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKATKASQEL
Sequence of entity 4 (G), FASTA
>8QYV_4 Histone H2B.1 (chains G)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Sequence of entity 5 (I), FASTA
>8QYV_5 DNA (118-MER) (chains I)
CCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTT
AAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTC
Sequence of entity 6 (J), FASTA
>8QYV_6 DNA (118-MER) (chains J)
GACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAA
GCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGG
Sequence of entity 7 (M), FASTA
>8QYV_7 Helicase SWR1 (chains M)
MTTSRKSHAKDKKAGGEQDLADLKFRYDLLTNELFHLREFVSLVDYDPTHFNDSESFQKF
LRETHLSLEERGEKFTDDVAKKGTNGDLTRRRRNLRTSTVVSSETTNEKKGDIELKLESI
APLVRNKCEELKYKLSDHSNRKSIVPQKRPIQHLKKREAAKSLKFKSERKENPLPLHEHI
AEERYDHIAKVEEPSEAFTIKCPSDDSSFENTSEHYSDNFYFTTSSEEEDIKKKRGRKKK
KPRIKLVVHPPKQTITNPLHVVKPGYESLHEYIASFKSLEDDLTLEEYNKYIDEQRRLLS
RLKKGIENGALKYDKETDSLQPITSKEIKTIITYKPDPISYFYKQQDLQIHTDHLINQGI
HMSKLFRSSTKARIARAKKVSQMIEQHFKHVAGAEERKAKEEERHKKSLARFAVQAVKKR
WNMAEKAYRILRKDEEEQLKRIEGKQHLSKMLEKSTQLLEAQLNQVNDDGRSSTPSSDSN
DVLSESDDDMDDELSTSSDEDEEVDADVGLENSPASTEATPTDESLNLIQLKEKYGHFNG
SSTVYDSRNKDEKFPTLDKHESSSSESSVMTGEESSIYSSSENESQNENDRESDDKTPSV
GLSALFGKGEESDGDLDLDDSEDFTVNSSSVEGEELEKDQVDNSAATFERAGDFVHTQNE
NRDDIKDVEEDAETKVQEEQLSVVDVPVPSLLRGNLRTYQKQGLNWLASLYNNHTNGILA
DEMGLGKTIQTISLLAYLACEKENWGPHLIVVPTSVLLNWEMEFKRFAPGFKVLTYYGSP
QQRKEKRKGWNKPDAFHVCIVSYQLVVQDQHSFKRKRWQYMVLDEAHNIKNFRSTRWQAL
LNFNTQRRLLLTGTPLQNNLAELWSLLYFLMPQTVIDGKKVSGFADLDAFQQWFGRPVDK
IIETGQNFGQDKETKKTVAKLHQVLRPYLLRRLKADVEKQMPAKYEHIVYCKLSKRQRFL
YDDFMSRAQTKATLASGNFMSIVNCLMQLRKVCNHPNLFEVRPILTSFVLEHCVASDYKD
VERTLLKLFKKNNQVNRVDLDFLNLVFTLNDKDLTSYHAEEISKLTCVKNFVEEVNKLRE
TNKQLQEEFGEASFLNFQDANQYFKYSNKQKLEGTVDMLNFLKMVNKLRCDRRPIFGKNL
IDLLTKDRRVKYDKSSIIDNELIKPLQTRVLDNRKIIDTFAVLTPSAVSLDMRKLALGLN
DDSSVGENTRLKVMQNCFEVSNPLHQLQTKLTIAFPDKSLLQYDCGKLQKLAILLQQLKD
NGHRALIFTQMTKVLDVLEQFLNYHGYLYMRLDGATKIEDRQILTERFNTDSRITVFILS
SRSGGLGINLTGADTVIFYDSDWNPAMDKQCQDRCHRIGQTRDVHIYRFVSEHTIESNIL
KKANQKRQLDNVVIQEGDFTTDYFSKLSVRDLLGSELPENASGGDKPLIADADVAAKDPR
QLERLLAQAEDEDDVKAANLAMREVEIDNDDFDESTEKKAANEEEENHAELDEYEGTAHV
DEYMIRFIANGYYY
Sequence of entity 8 (P), FASTA
>8QYV_8 SWR1-complex protein 5 (chains P)
MPEVETKIIPNEKEDEDEDGYIEEEDEDFQPEKDKLGGGSDDSDASDGGDDYDDGVNRDK
GRNKVDYSRIESESGGLIKTRRARQAEEEYAKTHKYESLTVESIPAKVNSIWEELQEASK
NRLLSSSGKVGSVLDGSKEARSTTAAQQEDKILIERNYKFAGETVHEKKWVSRSSAEGQE
YLNSLKFKQQAPAAPVQLEKAVRTKSNESRQHLRRPLKRPPLLEQIISGGLRPKLTTLEK
SQLDWASYVDRAGLNDELVLHNKDGFLARQEFLQRVGSAEDERYKELRRQQLAQQLQQDS
EAS
Sequence of entity 9 (R), FASTA
>8QYV_9 Actin-like protein ARP6 (chains R)
METPPIVIDNGSYEIKFGPSTNKKPFRALNALAKDKFGTSYLSNHIKNIKDISSITFRRP
HELGQLTLWELESCIWDYCLFNPSEFDGFDLKEGKGHHLVASESCMTLPELSKHADQVIF
EEYEFDSLFKSPVAVFVPFTKSYKGEMRTISGKDEDIDIVRGNSDSTNSTSSESKNAQDS
GSDYHDFQLVIDSGFNCTWIIPVLKGIPYYKAVKKLDIGGRFLTGLLKETLSFRHYNMMD
ETILVNNIKEQCLFVSPVSYFDSFKTKDKHALEYVLPDFQTSFLGYVRNPRKENVPLPED
AQIITLTDELFTIPETFFHPEISQITKPGIVEAILESLSMLPEIVRPLMVGNIVCTGGNF
NLPNFAQRLAAELQRQLPTDWTCHVSVPEGDCALFGWEVMSQFAKTDSYRKARVTREEYY
EHGPDWCTKHRFGYQNWI
Sequence of entity 10 (S), FASTA
>8QYV_10 Vacuolar protein sorting-associated protein 71 (chains S)
MKALVEEIDKKTYNPDIYFTSLDPQARRYTSKKINKQGTISTSRPVKRINYSLADLEARL
YTSRSEGDGNSISRQDDRNSKNSHSFEERYTQQEILQSDRRFMELNTENFSDLPNVPTLL
SDLTGVPRDRIESTTKPISQTSDGLSALMGGSSFVKEHSKYGHGWVLKPETLREIQLSYK
STKLPKPKRKNTNRIVALKKVLSSKRNLHSFLDSALLNLMDKNVIYHNVYNKRYFKVLPL
ITTCSICGGYDSISSCVNCGNKICSVSCFKLHNETRCRNR
Sequence of entity 11 (T, V, X), FASTA
>8QYV_11 RuvB-like protein 1 (chains T, V, X)
MVAISEVKENPGVNSSNSGAVTRTAAHTHIKGLGLDESGVAKRVEGGFVGQIEAREACGV
IVDLIKAKKMSGRAILLAGGPSTGKTALALAISQELGPKVPFCPLVGSELYSVEVKKTET
LMENFRRAIGLRIKETKEVYEGEVTELTPEDAENPLGGYGKTISHVIVGLKSAKGTKTLR
LDPTIYESIQREKVSIGDVIYIEANTGAVKRVGRSDAYATEFDLETEEYVPLPKGEVHKK
KEIVQDVTLHDLDVANARPQGGQDVISMMGQLLKPKKTEITEKLRQEVNKVVAKYIDQGV
AELIPGVLFIDEVNMLDIEIFTYLNKALESNIAPVVVLASNRGMTTVRGTEDVISPHGVP
PDLIDRLLIVRTLPYDKDEIRTIIERRATVERLQVESSALDLLATMGTETSLRYALQLLA
PCGILAQTSNRKEIVVNDVNEAKLLFLDAKRSTKILETSANYL
Sequence of entity 12 (U, W, Y), FASTA
>8QYV_12 RuvB-like protein 2 (chains U, W, Y)
MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKM
VQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQA
FRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLT
KEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS
LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHM
LDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYN
EQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEV
EDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAKSADPDAMDTTE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
| MG | Magnesium ion | Mg | 8 |
| BEF | Beryllium trifluoride ion | Be F3 | 2 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 8 |
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
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