6GEJ: Chromatin remodeller-nucleosome complex
Chromatin remodeller-nucleosome complex at 3.6 A resolution. Determined by electron microscopy at 3.6 Å resolution. Released 17 Oct 2018.
- Method
- Electron microscopy
- Resolution
- 3.6 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), synthetic construct
- Chains
- 20
- Atoms
- 43,702
- Mol. weight
- 783.85 kDa
- Ligands
- ZN, MG, BEF, ADP
- Released
- 17 Oct 2018
Explore 6GEJ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6GEJ contains 242 α-helices and 215 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.
Chains A and B: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-55 | 11 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 3 |
| α-helix | 89-113 | 25 | |
| β-strand | 118-119 | 2 | 4 |
| α-helix | 121-129 | 9 | |
Chains C and D: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 6 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 5 |
| α-helix | 83-91 | 9 | |
| β-strand | 97 | 1 | 7 |
Chains E and F: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 28-37 | 10 | |
| β-strand | 43-44 | 2 | 9 |
| α-helix | 48-73 | 26 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 102 | 1 | 7 |
Chain G: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56-57 | 2 | 10 |
| α-helix | 59-86 | 28 | |
| β-strand | 91-92 | 2 | 9 |
| α-helix | 94-104 | 11 | |
| α-helix | 107-125 | 19 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56-57 | 2 | 12 |
| α-helix | 59-86 | 28 | |
| β-strand | 91-92 | 2 | 11 |
| α-helix | 94-104 | 11 | |
| α-helix | 107-124 | 18 | |
Chain M: 30 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 698-711 | 14 | |
| β-strand | 718-721 | 4 | 13 |
| α-helix | 727-741 | 15 | |
| β-strand | 749-752 | 4 | 13 |
| α-helix | 757-766 | 10 | |
| β-strand | 773 | 1 | 14 |
| α-helix | 782-786 | 5 | |
| β-strand | 798 | 1 | 14 |
| β-strand | 800-802 | 3 | 13 |
| α-helix | 805-808 | 4 | |
| α-helix | 810-813 | 4 | |
| β-strand | 820-824 | 5 | 13 |
| α-helix | 835-841 | 7 | |
| β-strand | 847-851 | 5 | 13 |
| α-helix | 860-870 | 11 | |
| α-helix | 914-924 | 11 | |
| β-strand | 930-932 | 3 | 13 |
| β-strand | 944-946 | 3 | 15 |
| β-strand | 949-951 | 3 | 16 |
| α-helix | 955-970 | 16 | |
| α-helix | 972-974 | 3 | |
| α-helix | 979-993 | 15 | |
| α-helix | 1014-1029 | 16 | |
| α-helix | 1047-1049 | 3 | |
| α-helix | 1057-1064 | 8 | |
| β-strand | 1066 | 1 | 17 |
| α-helix | 1070-1093 | 24 | |
| α-helix | 1104-1132 | 29 | |
| α-helix | 1142-1146 | 5 | |
| α-helix | 1160-1163 | 4 | |
| α-helix | 1166-1172 | 7 | |
| α-helix | 1174-1180 | 7 | |
| α-helix | 1192-1197 | 6 | |
| α-helix | 1207-1219 | 13 | |
| α-helix | 1225-1232 | 8 | |
| α-helix | 1240-1243 | 4 | |
| α-helix | 1251-1260 | 10 | |
| β-strand | 1265-1269 | 5 | 15 |
| α-helix | 1273-1285 | 13 | |
| β-strand | 1289-1291 | 3 | 15 |
| α-helix | 1299-1309 | 11 | |
| β-strand | 1316-1320 | 5 | 15 |
| β-strand | 1335-1338 | 4 | 15 |
| α-helix | 1349-1355 | 7 | |
| β-strand | 1364-1366 | 3 | 15 |
| β-strand | 1369-1371 | 3 | 16 |
| α-helix | 1375-1385 | 11 | |
Chain R: 24 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-9 | 4 | 18 |
| β-strand | 14-19 | 6 | 18 |
| α-helix | 25 | 1 | |
| β-strand | 26-29 | 4 | 18 |
| β-strand | 32-35 | 4 | 19 |
| β-strand | 40-41 | 2 | 19 |
| α-helix | 46-48 | 3 | |
| β-strand | 55-58 | 4 | 19 |
| β-strand | 61 | 1 | 20 |
| β-strand | 66 | 1 | 20 |
| α-helix | 69-81 | 13 | |
| β-strand | 98-102 | 5 | 18 |
| α-helix | 109-117 | 9 | |
| α-helix | 118-122 | 5 | |
| β-strand | 127-130 | 4 | 18 |
| α-helix | 133-136 | 4 | |
| α-helix | 137-142 | 6 | |
| β-strand | 147-151 | 5 | 21 |
| β-strand | 188-192 | 5 | 21 |
| β-strand | 198-204 | 7 | 21 |
| β-strand | 207-208 | 2 | 21 |
| β-strand | 214-216 | 3 | 21 |
| α-helix | 220-234 | 15 | |
| α-helix | 242-252 | 11 | |
| α-helix | 260-265 | 6 | |
| β-strand | 272-275 | 4 | 22 |
| α-helix | 276-278 | 3 | |
| β-strand | 286-288 | 3 | 22 |
| α-helix | 302 | 1 | |
| β-strand | 303-306 | 4 | 22 |
| α-helix | 308-312 | 5 | |
| α-helix | 314-316 | 3 | |
| α-helix | 320-323 | 4 | |
| α-helix | 330-339 | 10 | |
| α-helix | 346-349 | 4 | |
| β-strand | 353-356 | 4 | 21 |
| α-helix | 359-361 | 3 | |
| α-helix | 365-376 | 12 | |
| β-strand | 378 | 1 | 23 |
| β-strand | 384-388 | 5 | 21 |
| α-helix | 392-405 | 14 | |
| α-helix | 408-412 | 5 | |
| β-strand | 415 | 1 | 18 |
| α-helix | 416-421 | 6 | |
| α-helix | 424-426 | 3 | |
| α-helix | 427-431 | 5 | |
Chain S: 12 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-7 | 3 | 24 |
| β-strand | 18-21 | 4 | 25 |
| α-helix | 53-60 | 8 | |
| α-helix | 92-106 | 15 | |
| α-helix | 116-124 | 9 | |
| α-helix | 128-134 | 7 | |
| α-helix | 169-178 | 10 | |
| α-helix | 179-181 | 3 | |
| α-helix | 193-202 | 10 | |
| α-helix | 208-213 | 6 | |
| α-helix | 219-222 | 4 | |
| α-helix | 223-227 | 5 | |
| α-helix | 239-240 | 2 | |
| β-strand | 255 | 1 | 25 |
| β-strand | 262 | 1 | 25 |
| α-helix | 266-272 | 7 | |
7 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 |
|---|
| Vacuolar protein sorting-associated protein 72 | Z | protein | 131 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | |
| Histone H3 | A, B | protein | 136 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P61830 (AlphaFold model) |
| Histone H4 | C, D | protein | 103 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P02309 (AlphaFold model) |
| Histone H2A.1 | E, F | protein | 132 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P04911 (AlphaFold model) |
| Histone H2B.1 | G, H | protein | 131 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P02293 (AlphaFold model) |
| DNA (154-mer) | I | DNA | 154 | synthetic construct | |
| DNA (154-mer) | J | DNA | 154 | synthetic construct | |
| Helicase SWR1 | M | protein | 1514 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q05471 |
| Actin-like protein ARP6 | R | protein | 438 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q12509 |
| Vacuolar protein sorting-associated protein 71 | S | protein | 280 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q03433 |
| RuvB-like protein 1 | T, V, X | protein | 463 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q03940 |
| RuvB-like protein 2 | U, W, Y | protein | 471 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q12464 |
Sequence of entity 1 (Z), FASTA
>6GEJ_1 Vacuolar protein sorting-associated protein 72 (chains Z)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXX
Sequence of entity 2 (A, B), FASTA
>6GEJ_2 Histone H3 (chains A, B)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKEIKLARRLRGERS
Sequence of entity 3 (C, D), FASTA
>6GEJ_3 Histone H4 (chains C, D)
MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLK
SFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
Sequence of entity 4 (E, F), FASTA
>6GEJ_4 Histone H2A.1 (chains E, F)
MSGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKATKASQEL
Sequence of entity 5 (G, H), FASTA
>6GEJ_5 Histone H2B.1 (chains G, H)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Sequence of entity 6 (I), FASTA
>6GEJ_6 DNA (154-MER) (chains I)
CGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGC
TTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTC
TCCAGGCACGTGTCAGATATATACATCCTGTGCA
Sequence of entity 7 (J), FASTA
>6GEJ_7 DNA (154-MER) (chains J)
TGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGT
TAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAA
TTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCG
Sequence of entity 8 (M), FASTA
>6GEJ_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
>6GEJ_9 Actin-like protein ARP6 (chains R)
METPPIVIDNGSYEIKFGPSTNKKPFRALNALAKDKFGTSYLSNHIKNIKDISSITFRRP
HELGQLTLWELESCIWDYCLFNPSEFDGFDLKEGKGHHLVASESCMTLPELSKHADQVIF
EEYEFDSLFKSPVAVFVPFTKSYKGEMRTISGKDEDIDIVRGNSDSTNSTSSESKNAQDS
GSDYHDFQLVIDSGFNCTWIIPVLKGIPYYKAVKKLDIGGRFLTGLLKETLSFRHYNMMD
ETILVNNIKEQCLFVSPVSYFDSFKTKDKHALEYVLPDFQTSFLGYVRNPRKENVPLPED
AQIITLTDELFTIPETFFHPEISQITKPGIVEAILESLSMLPEIVRPLMVGNIVCTGGNF
NLPNFAQRLAAELQRQLPTDWTCHVSVPEGDCALFGWEVMSQFAKTDSYRKARVTREEYY
EHGPDWCTKHRFGYQNWI
Sequence of entity 10 (S), FASTA
>6GEJ_10 Vacuolar protein sorting-associated protein 71 (chains S)
MKALVEEIDKKTYNPDIYFTSLDPQARRYTSKKINKQGTISTSRPVKRINYSLADLEARL
YTSRSEGDGNSISRQDDRNSKNSHSFEERYTQQEILQSDRRFMELNTENFSDLPNVPTLL
SDLTGVPRDRIESTTKPISQTSDGLSALMGGSSFVKEHSKYGHGWVLKPETLREIQLSYK
STKLPKPKRKNTNRIVALKKVLSSKRNLHSFLDSALLNLMDKNVIYHNVYNKRYFKVLPL
ITTCSICGGYDSISSCVNCGNKICSVSCFKLHNETRCRNR
Sequence of entity 11 (T, V, X), FASTA
>6GEJ_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
>6GEJ_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
Structure and dynamics of the yeast SWR1-nucleosome complex. Willhoft, O., Ghoneim, M., Lin, C.L. et al. Science (2018) 362. DOI 10.1126/science.aat7716 · 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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