8QKU: SWR1-nucleosome complex in configuration 1
SWR1-nucleosome complex in configuration 1. 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
- 20
- Atoms
- 45,395
- Mol. weight
- 814.96 kDa
- Ligands
- ADP, BEF, MG, ZN
- Released
- 2 Oct 2024
Explore 8QKU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8QKU contains 242 α-helices and 209 β-strands across 18 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, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-55 | 11 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83 | 1 | 1 |
| α-helix | 90-113 | 24 | |
| α-helix | 121-131 | 11 | |
Chain B: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-55 | 11 | |
| α-helix | 64-78 | 15 | |
| β-strand | 84 | 1 | 2 |
| α-helix | 90-113 | 24 | |
| α-helix | 121-131 | 11 | |
Chain C: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| α-helix | 50-75 | 26 | |
| β-strand | 81 | 1 | 2 |
| α-helix | 83-91 | 9 | |
| β-strand | 97 | 1 | 3 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| α-helix | 48-75 | 28 | |
| β-strand | 80 | 1 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 97 | 1 | 4 |
Chain E: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 28-36 | 9 | |
| β-strand | 43-44 | 2 | 5 |
| α-helix | 47-72 | 26 | |
| β-strand | 78-79 | 2 | 6 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 102 | 1 | 3 |
Chain F: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 28-37 | 10 | |
| β-strand | 43-44 | 2 | 7 |
| α-helix | 47-73 | 27 | |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 102 | 1 | 4 |
| α-helix | 114-116 | 3 | |
Chain G: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56-57 | 2 | 6 |
| α-helix | 59-86 | 28 | |
| β-strand | 91-92 | 2 | 5 |
| α-helix | 94-104 | 11 | |
| α-helix | 107-127 | 21 | |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| α-helix | 59-86 | 28 | |
| β-strand | 91-92 | 2 | 7 |
| α-helix | 94-104 | 11 | |
| α-helix | 107-124 | 18 | |
10 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.2 | E, F | protein | 158 | Saccharomyces cerevisiae S288C | P04912 (AlphaFold model) |
| Histone H2B.1 | G, H | protein | 131 | Saccharomyces cerevisiae S288C | P02293 (AlphaFold model) |
| DNA (177-mer) | I | DNA | 177 | synthetic construct | |
| DNA (177-mer) | J | DNA | 177 | synthetic construct | |
| Helicase SWR1 | M | protein | 1514 | Saccharomyces cerevisiae S288C | Q05471 |
| 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 |
| Vacuolar protein sorting-associated protein 72 | Z | protein | 180 | Saccharomyces cerevisiae S288C | Q03388 |
Sequence of entity 1 (A, B), FASTA
>8QKU_1 Histone H3 (chains A, B)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKEIKLARRLRGERS
Sequence of entity 2 (C, D), FASTA
>8QKU_2 Histone H4 (chains C, D)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
Sequence of entity 3 (E, F), FASTA
>8QKU_3 Histone H2A.2 (chains E, F)
MSGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKTAKEVCQDCQSFSRTVRTELKRNKANQTFLSFGV
Sequence of entity 4 (G, H), FASTA
>8QKU_4 Histone H2B.1 (chains G, H)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Sequence of entity 5 (I), FASTA
>8QKU_5 DNA (177-MER) (chains I)
GCATTAATGCATCCGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCG
TAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCA
AGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTA
Sequence of entity 6 (J), FASTA
>8QKU_6 DNA (177-MER) (chains J)
TACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGG
CGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGA
CCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGCGGATGCATTAATGC
Sequence of entity 7 (M), FASTA
>8QKU_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 (R), FASTA
>8QKU_8 Actin-like protein ARP6 (chains R)
METPPIVIDNGSYEIKFGPSTNKKPFRALNALAKDKFGTSYLSNHIKNIKDISSITFRRP
HELGQLTLWELESCIWDYCLFNPSEFDGFDLKEGKGHHLVASESCMTLPELSKHADQVIF
EEYEFDSLFKSPVAVFVPFTKSYKGEMRTISGKDEDIDIVRGNSDSTNSTSSESKNAQDS
GSDYHDFQLVIDSGFNCTWIIPVLKGIPYYKAVKKLDIGGRFLTGLLKETLSFRHYNMMD
ETILVNNIKEQCLFVSPVSYFDSFKTKDKHALEYVLPDFQTSFLGYVRNPRKENVPLPED
AQIITLTDELFTIPETFFHPEISQITKPGIVEAILESLSMLPEIVRPLMVGNIVCTGGNF
NLPNFAQRLAAELQRQLPTDWTCHVSVPEGDCALFGWEVMSQFAKTDSYRKARVTREEYY
EHGPDWCTKHRFGYQNWI
Sequence of entity 9 (S), FASTA
>8QKU_9 Vacuolar protein sorting-associated protein 71 (chains S)
MKALVEEIDKKTYNPDIYFTSLDPQARRYTSKKINKQGTISTSRPVKRINYSLADLEARL
YTSRSEGDGNSISRQDDRNSKNSHSFEERYTQQEILQSDRRFMELNTENFSDLPNVPTLL
SDLTGVPRDRIESTTKPISQTSDGLSALMGGSSFVKEHSKYGHGWVLKPETLREIQLSYK
STKLPKPKRKNTNRIVALKKVLSSKRNLHSFLDSALLNLMDKNVIYHNVYNKRYFKVLPL
ITTCSICGGYDSISSCVNCGNKICSVSCFKLHNETRCRNR
Sequence of entity 10 (T, V, X), FASTA
>8QKU_10 RuvB-like protein 1 (chains T, V, X)
MVAISEVKENPGVNSSNSGAVTRTAAHTHIKGLGLDESGVAKRVEGGFVGQIEAREACGV
IVDLIKAKKMSGRAILLAGGPSTGKTALALAISQELGPKVPFCPLVGSELYSVEVKKTET
LMENFRRAIGLRIKETKEVYEGEVTELTPEDAENPLGGYGKTISHVIVGLKSAKGTKTLR
LDPTIYESIQREKVSIGDVIYIEANTGAVKRVGRSDAYATEFDLETEEYVPLPKGEVHKK
KEIVQDVTLHDLDVANARPQGGQDVISMMGQLLKPKKTEITEKLRQEVNKVVAKYIDQGV
AELIPGVLFIDEVNMLDIEIFTYLNKALESNIAPVVVLASNRGMTTVRGTEDVISPHGVP
PDLIDRLLIVRTLPYDKDEIRTIIERRATVERLQVESSALDLLATMGTETSLRYALQLLA
PCGILAQTSNRKEIVVNDVNEAKLLFLDAKRSTKILETSANYL
Sequence of entity 11 (U, W, Y), FASTA
>8QKU_11 RuvB-like protein 2 (chains U, W, Y)
MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKM
VQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQA
FRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLT
KEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS
LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHM
LDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYN
EQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEV
EDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAKSADPDAMDTTE
Sequence of entity 12 (Z), FASTA
>8QKU_12 Vacuolar protein sorting-associated protein 72 (chains Z)
KRSSVMENTMKVYEKLSKAEKKRKIIQERIRKHKEQESQHMLTQEERLRIAKETEKLNIL
SLDKFKEQEVWKKENRLALQKRQKQKFQPNETILQFLSTAWLMTPAMELEDRKYWQEQLN
KRDKKKKKYPRKPKKTQTYEGPEQLTSRNFVTLYDFPNAPPNLKDFNTNLFGDRWSYTNG
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
Nucleosome flipping drives kinetic proofreading and processivity by SWR1. Girvan, P., Jalal, A.S.B., McCormack, E.A. et al. Nature (2024) 636:251-257. DOI 10.1038/s41586-024-08152-y · 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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