9FBW: SWR1 lacking Swc5 subunit
SWR1 lacking Swc5 subunit in complex with hexasome. Determined by electron microscopy at 4.4 Å resolution. Released 2 Oct 2024.
- Method
- Electron microscopy
- Resolution
- 4.4 Å
- Organisms
- Saccharomyces cerevisiae S288C, synthetic construct
- Chains
- 18
- Atoms
- 39,683
- Mol. weight
- 809.14 kDa
- Ligands
- ZN, MG, BEF, ADP
- Released
- 2 Oct 2024
Explore 9FBW in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9FBW contains 208 α-helices and 178 β-strands across 16 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: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-75 | 12 | |
| α-helix | 91-113 | 23 | |
| α-helix | 121-129 | 9 | |
Chain B: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-54 | 9 | |
| α-helix | 65-75 | 11 | |
| α-helix | 88-113 | 26 | |
| α-helix | 121-129 | 9 | |
Chain C: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-40 | 9 | |
| α-helix | 51-75 | 25 | |
| α-helix | 85-93 | 9 | |
| β-strand | 98 | 1 | 1 |
Chain D: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| α-helix | 41-44 | 4 | |
| α-helix | 47-53 | 7 | |
| α-helix | 58-74 | 17 | |
| α-helix | 83-86 | 4 | |
Chain E: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-36 | 8 | |
| α-helix | 51-72 | 22 | |
| α-helix | 81-90 | 10 | |
| α-helix | 93-97 | 5 | |
| β-strand | 103 | 1 | 1 |
| α-helix | 108-110 | 3 | |
Chain G: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| α-helix | 59-79 | 21 | |
| α-helix | 83-85 | 3 | |
| α-helix | 94-104 | 11 | |
Chain M: 31 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 698-711 | 14 | |
| β-strand | 718 | 1 | 2 |
| α-helix | 721-722 | 2 | |
| α-helix | 727-741 | 15 | |
| β-strand | 748-750 | 3 | 3 |
| α-helix | 754-756 | 3 | |
| α-helix | 758-766 | 9 | |
| α-helix | 784-786 | 3 | |
| β-strand | 798-800 | 3 | 3 |
| α-helix | 803-808 | 6 | |
| β-strand | 824 | 1 | 4 |
| α-helix | 835-841 | 7 | |
| β-strand | 850 | 1 | 2 |
| β-strand | 851 | 1 | 4 |
| α-helix | 860-870 | 11 | |
| α-helix | 915-925 | 11 | |
| β-strand | 944-950 | 7 | 5 |
| α-helix | 952-954 | 3 | |
| α-helix | 955-971 | 17 | |
| α-helix | 981-989 | 9 | |
| β-strand | 1008-1010 | 3 | 6 |
| α-helix | 1016-1027 | 12 | |
| α-helix | 1047-1049 | 3 | |
| α-helix | 1051-1053 | 3 | |
| α-helix | 1056-1064 | 9 | |
| α-helix | 1072-1087 | 16 | |
| α-helix | 1105-1132 | 28 | |
| α-helix | 1141-1145 | 5 | |
| α-helix | 1166-1172 | 7 | |
| α-helix | 1174-1177 | 4 | |
| β-strand | 1187-1189 | 3 | 6 |
| α-helix | 1194-1197 | 4 | |
| α-helix | 1210-1218 | 9 | |
| α-helix | 1225-1229 | 5 | |
| α-helix | 1249-1260 | 12 | |
| β-strand | 1265-1269 | 5 | 5 |
| α-helix | 1272-1275 | 4 | |
| α-helix | 1278-1285 | 8 | |
| β-strand | 1289-1292 | 4 | 5 |
| α-helix | 1302-1309 | 8 | |
| β-strand | 1316-1320 | 5 | 5 |
| β-strand | 1335-1337 | 3 | 5 |
| α-helix | 1348-1355 | 8 | |
| β-strand | 1364-1370 | 7 | 5 |
| α-helix | 1383-1386 | 4 | |
Chain R: 21 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-9 | 4 | 7 |
| β-strand | 15-17 | 3 | 7 |
| β-strand | 19 | 1 | 7 |
| β-strand | 26-28 | 3 | 7 |
| β-strand | 34 | 1 | 8 |
| β-strand | 40 | 1 | 8 |
| β-strand | 56 | 1 | 8 |
| β-strand | 61 | 1 | 9 |
| β-strand | 66 | 1 | 9 |
| α-helix | 72-80 | 9 | |
| β-strand | 98 | 1 | 10 |
| β-strand | 99-102 | 4 | 7 |
| α-helix | 109-117 | 9 | |
| α-helix | 118-122 | 5 | |
| β-strand | 127 | 1 | 10 |
| α-helix | 133-136 | 4 | |
| α-helix | 137-140 | 4 | |
| β-strand | 149-150 | 2 | 11 |
| β-strand | 188-193 | 6 | 11 |
| β-strand | 198-204 | 7 | 11 |
| β-strand | 207-208 | 2 | 11 |
| α-helix | 210-212 | 3 | |
| β-strand | 214-216 | 3 | 11 |
| α-helix | 220-232 | 13 | |
| α-helix | 242-252 | 11 | |
| α-helix | 261-264 | 4 | |
| β-strand | 273-275 | 3 | 12 |
| α-helix | 276-277 | 2 | |
| β-strand | 286-288 | 3 | 12 |
| β-strand | 303-305 | 3 | 12 |
| α-helix | 312-318 | 7 | |
| α-helix | 320-323 | 4 | |
| α-helix | 330-340 | 11 | |
| α-helix | 346-350 | 5 | |
| β-strand | 353-357 | 5 | 11 |
| α-helix | 358-361 | 4 | |
| α-helix | 365-376 | 12 | |
| β-strand | 385-386 | 2 | 11 |
| α-helix | 392-405 | 14 | |
| α-helix | 409-411 | 3 | |
| α-helix | 424-426 | 3 | |
| α-helix | 427-431 | 5 | |
| α-helix | 434-437 | 4 | |
8 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 (112-mer) | I | DNA | 112 | synthetic construct | |
| DNA (112-mer) | J | DNA | 112 | 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 | 795 | Saccharomyces cerevisiae S288C | Q03388 |
Sequence of entity 1 (A, B), FASTA
>9FBW_1 Histone H3 (chains A, B)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKEIKLARRLRGERS
Sequence of entity 2 (C, D), FASTA
>9FBW_2 Histone H4 (chains C, D)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
Sequence of entity 3 (E), FASTA
>9FBW_3 Histone H2A.1 (chains E)
MSGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKATKASQEL
Sequence of entity 4 (G), FASTA
>9FBW_4 Histone H2B.1 (chains G)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Sequence of entity 5 (I), FASTA
>9FBW_5 DNA (112-MER) (chains I)
CCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTT
AAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCC
Sequence of entity 6 (J), FASTA
>9FBW_6 DNA (112-MER) (chains J)
GGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTG
CTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGG
Sequence of entity 7 (M), FASTA
>9FBW_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
>9FBW_8 Actin-like protein ARP6 (chains R)
METPPIVIDNGSYEIKFGPSTNKKPFRALNALAKDKFGTSYLSNHIKNIKDISSITFRRP
HELGQLTLWELESCIWDYCLFNPSEFDGFDLKEGKGHHLVASESCMTLPELSKHADQVIF
EEYEFDSLFKSPVAVFVPFTKSYKGEMRTISGKDEDIDIVRGNSDSTNSTSSESKNAQDS
GSDYHDFQLVIDSGFNCTWIIPVLKGIPYYKAVKKLDIGGRFLTGLLKETLSFRHYNMMD
ETILVNNIKEQCLFVSPVSYFDSFKTKDKHALEYVLPDFQTSFLGYVRNPRKENVPLPED
AQIITLTDELFTIPETFFHPEISQITKPGIVEAILESLSMLPEIVRPLMVGNIVCTGGNF
NLPNFAQRLAAELQRQLPTDWTCHVSVPEGDCALFGWEVMSQFAKTDSYRKARVTREEYY
EHGPDWCTKHRFGYQNWI
Sequence of entity 9 (S), FASTA
>9FBW_9 Vacuolar protein sorting-associated protein 71 (chains S)
MKALVEEIDKKTYNPDIYFTSLDPQARRYTSKKINKQGTISTSRPVKRINYSLADLEARL
YTSRSEGDGNSISRQDDRNSKNSHSFEERYTQQEILQSDRRFMELNTENFSDLPNVPTLL
SDLTGVPRDRIESTTKPISQTSDGLSALMGGSSFVKEHSKYGHGWVLKPETLREIQLSYK
STKLPKPKRKNTNRIVALKKVLSSKRNLHSFLDSALLNLMDKNVIYHNVYNKRYFKVLPL
ITTCSICGGYDSISSCVNCGNKICSVSCFKLHNETRCRNR
Sequence of entity 10 (T, V, X), FASTA
>9FBW_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
>9FBW_11 RuvB-like protein 2 (chains U, W, Y)
MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKM
VQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQA
FRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLT
KEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS
LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHM
LDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYN
EQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEV
EDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAKSADPDAMDTTE
Sequence of entity 12 (Z), FASTA
>9FBW_12 Vacuolar protein sorting-associated protein 72 (chains Z)
MSDEGADKSLDTNTEFIIQTRSRRSNAGNKLQKLLEQELRDIESTKRQISSYKNGNDDEE
DEIGLLFQEDEDDEDFEMMAKDDDDEGEEKEDETQSIRKEPSQASSEQAADDLMFSSSES
EDSSNENDEDAEEKEIRRQELLSRKKRNKRLQKGPVVIKKQKPKPKSGEAIPRSHHTHEQ
LNAETLLLNTRRTSKRSSVMENTMKVYEKLSKAEKKRKIIQERIRKHKEQESQHMLTQEE
RLRIAKETEKLNILSLDKFKEQEVWKKENRLALQKRQKQKFQPNETILQFLSTAWLMTPA
MELEDRKYWQEQLNKRDKKKKKYPRKPKKNLNLGKQDASDDKKRESEESIKNDGDVNSLG
ENSSSVHNQKRIEETSTNDTVEGESSPDAAVSRVNSDELKPTALPDVTLDAIANKQSTVD
EAPNSQPQKNIITNEQKITNVGEPIQNLHNEEIKDEMVSALESRENTFENSSPAAQVVSQ
RDNSATPTPSNSTGTEDTILISPDTDIKGEPEPCLKTEGIENLSHNVPQETKSNTDVSFL
KQVTFTDHPQVAIIDTEESPSKKDTANVDESSAENSLSTQTYEGPEQLTSRNFVTLYDFP
NAPPNLKDFNTNLFGDRWSYTNGLSATQRPQDMKTVFHSILPSPPQSSVPSPTVDISLDL
SALANFPSFGEYDKKIVHQINTEINKDLEIKIKTQPPTGVFLANGIRKKCLITNKECQYF
DPRTGVPYSDVEAYKIIQRIQDPISKEEGRSDIKRDETTNEDSDDQVRFKWFGFKNGGIY
LDLSQRPAKGVPEGF
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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