8QKV: SWR1-nucleosome complex in configuration 2
SWR1-nucleosome complex in configuration 2. Determined by electron microscopy at 4.7 Å resolution. Released 2 Oct 2024.
- Method
- Electron microscopy
- Resolution
- 4.7 Å
- Organisms
- Saccharomyces cerevisiae S288C, synthetic construct
- Chains
- 20
- Atoms
- 45,846
- Mol. weight
- 825.47 kDa
- Ligands
- ADP, ZN, MG, BEF
- Released
- 2 Oct 2024
Explore 8QKV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8QKV contains 227 α-helices and 184 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, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 2 |
| α-helix | 90-113 | 24 | |
| β-strand | 118-119 | 2 | 1 |
| α-helix | 121-129 | 9 | |
Chain B: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 46-56 | 11 | |
| α-helix | 64-78 | 15 | |
| α-helix | 90-113 | 24 | |
| α-helix | 121-130 | 10 | |
Chain C: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-39 | 9 | |
| α-helix | 50-75 | 26 | |
| α-helix | 81-82 | 2 | |
| α-helix | 83-91 | 9 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 1 |
| α-helix | 48-75 | 28 | |
| β-strand | 80-81 | 2 | 2 |
| α-helix | 83-92 | 10 | |
Chain E: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-36 | 9 | |
| α-helix | 47-72 | 26 | |
| α-helix | 81-89 | 9 | |
| α-helix | 92-97 | 6 | |
| α-helix | 102-103 | 2 | |
Chain F: 6 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 28-37 | 10 | |
| β-strand | 43-44 | 2 | 3 |
| α-helix | 47-73 | 27 | |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| α-helix | 114-116 | 3 | |
Chain G: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| α-helix | 59-86 | 28 | |
| 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 | 3 |
| 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 (194-mer) | I | DNA | 194 | synthetic construct | |
| DNA (194-mer) | J | DNA | 194 | synthetic construct | |
| Vacuolar protein sorting-associated protein 72 | Z | protein | 180 | Saccharomyces cerevisiae S288C | Q03388 |
| 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 |
Sequence of entity 1 (A, B), FASTA
>8QKV_1 Histone H3 (chains A, B)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKEIKLARRLRGERS
Sequence of entity 2 (C, D), FASTA
>8QKV_2 Histone H4 (chains C, D)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
Sequence of entity 3 (E, F), FASTA
>8QKV_3 Histone H2A.2 (chains E, F)
MSGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKTAKEVCQDCQSFSRTVRTELKRNKANQTFLSFGV
Sequence of entity 4 (G, H), FASTA
>8QKV_4 Histone H2B.1 (chains G, H)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Sequence of entity 5 (I), FASTA
>8QKV_5 DNA (194-MER) (chains I)
TCCGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCT
AGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACT
CCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTACTCGGGGTGGCGAT
AAGTCGTGTCTTAC
Sequence of entity 6 (J), FASTA
>8QKV_6 DNA (194-MER) (chains J)
GTAAGACACGACTTATCGCCACCCCGAGTACATGCACAGGATGTATATATCTGACACGTG
CCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGC
GTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCC
AGGGCGGCCGCGGA
Sequence of entity 7 (Z), FASTA
>8QKV_7 Vacuolar protein sorting-associated protein 72 (chains Z)
KRSSVMENTMKVYEKLSKAEKKRKIIQERIRKHKEQESQHMLTQEERLRIAKETEKLNIL
SLDKFKEQEVWKKENRLALQKRQKQKFQPNETILQFLSTAWLMTPAMELEDRKYWQEQLN
KRDKKKKKYPRKPKKTQTYEGPEQLTSRNFVTLYDFPNAPPNLKDFNTNLFGDRWSYTNG
Sequence of entity 8 (M), FASTA
>8QKV_8 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 9 (R), FASTA
>8QKV_9 Actin-like protein ARP6 (chains R)
METPPIVIDNGSYEIKFGPSTNKKPFRALNALAKDKFGTSYLSNHIKNIKDISSITFRRP
HELGQLTLWELESCIWDYCLFNPSEFDGFDLKEGKGHHLVASESCMTLPELSKHADQVIF
EEYEFDSLFKSPVAVFVPFTKSYKGEMRTISGKDEDIDIVRGNSDSTNSTSSESKNAQDS
GSDYHDFQLVIDSGFNCTWIIPVLKGIPYYKAVKKLDIGGRFLTGLLKETLSFRHYNMMD
ETILVNNIKEQCLFVSPVSYFDSFKTKDKHALEYVLPDFQTSFLGYVRNPRKENVPLPED
AQIITLTDELFTIPETFFHPEISQITKPGIVEAILESLSMLPEIVRPLMVGNIVCTGGNF
NLPNFAQRLAAELQRQLPTDWTCHVSVPEGDCALFGWEVMSQFAKTDSYRKARVTREEYY
EHGPDWCTKHRFGYQNWI
Sequence of entity 10 (S), FASTA
>8QKV_10 Vacuolar protein sorting-associated protein 71 (chains S)
MKALVEEIDKKTYNPDIYFTSLDPQARRYTSKKINKQGTISTSRPVKRINYSLADLEARL
YTSRSEGDGNSISRQDDRNSKNSHSFEERYTQQEILQSDRRFMELNTENFSDLPNVPTLL
SDLTGVPRDRIESTTKPISQTSDGLSALMGGSSFVKEHSKYGHGWVLKPETLREIQLSYK
STKLPKPKRKNTNRIVALKKVLSSKRNLHSFLDSALLNLMDKNVIYHNVYNKRYFKVLPL
ITTCSICGGYDSISSCVNCGNKICSVSCFKLHNETRCRNR
Sequence of entity 11 (T, V, X), FASTA
>8QKV_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
>8QKV_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 |
| ZN | Zinc ion | Zn | 2 |
| MG | Magnesium ion | Mg | 8 |
| BEF | Beryllium trifluoride ion | Be F3 | 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
About this viewer
MolViewer shows 8QKV 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.