9B1D: Native SWR1

Cryo-EM structure of native SWR1 bound to DNA (composite structure). Determined by electron microscopy at 3.3 Å resolution. Released 9 Oct 2024.

Method
Electron microscopy
Resolution
3.3 Å
Organisms
Saccharomyces cerevisiae W303, synthetic construct
Chains
12
Atoms
33,147
Mol. weight
875.08 kDa
Ligands
AGS, ADP, ZN, MG
Released
9 Oct 2024

Explore 9B1D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B1D contains 207 α-helices and 208 β-strands across 10 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: 40 helices, 19 β-strands

ElementResiduesLengthSheet
α-helix686-6894
α-helix698-71215
β-strand717-71931
α-helix721-7222
α-helix727-74115
β-strand748-75141
α-helix754-76714
β-strand773-77531
α-helix780-7878
β-strand798-80141
α-helix803-81311
β-strand818-82361
α-helix826-8294
α-helix835-8417
β-strand845-85171
α-helix860-87011
β-strand874-87632
β-strand879-88132
α-helix887-8904
α-helix891-8955
α-helix896-9038
α-helix912-92514
α-helix934-9374
β-strand944-95183
α-helix955-96915
α-helix983-99412
α-helix996-9983
α-helix1001-10033
β-strand100614
β-strand1008-100925
α-helix1016-10183
α-helix1019-103517
α-helix1050-10534
α-helix1056-10649
β-strand106616
α-helix1068-108922
α-helix1095-10973
α-helix1100-113031
α-helix1138-11458
α-helix1159-11624
α-helix1166-11727
α-helix1174-11807
β-strand1187-118825
α-helix1191-11955
α-helix1207-121913
α-helix1225-12328
β-strand123314
α-helix1239-12435
α-helix1246-126116
β-strand1265-126953
α-helix1272-128413
β-strand1289-129133
α-helix1298-131013
β-strand1316-132053
α-helix1322-13254
β-strand1335-133843
α-helix1345-135511
β-strand1364-137183
α-helix1375-139420
Chain B: 4 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix238-27841
β-strand286-296117
α-helix299-31517
β-strand588-598117
β-strand60217
α-helix606-6149
β-strand635-64068
α-helix658-6647
Chain C: 24 helices, 23 β-strands
ElementResiduesLengthSheet
α-helix4-52
β-strand6-1059
β-strand15-1959
β-strand32-34310
β-strand40-42310
α-helix43-486
β-strand56-58310
β-strand61111
β-strand66111
α-helix69-8113
β-strand98-10149
α-helix109-1179
α-helix118-1225
β-strand127-13049
α-helix133-1364
α-helix137-1426
β-strand147-151512
β-strand187-193712
β-strand198-204712
β-strand207-208212
β-strand214-216312
α-helix220-23415
α-helix242-25110
α-helix260-2656
β-strand272-275413
α-helix276-2772
β-strand278114
β-strand282114
β-strand286-288313
α-helix295-2984
β-strand303-306413
α-helix309-3124
α-helix314-3174
α-helix320-3234
α-helix330-34011
α-helix346-3516
β-strand353-356412
α-helix359-3613
α-helix365-37612
β-strand378115
β-strand384-388512
α-helix393-40412
α-helix407-4126
β-strand414-41529
α-helix416-4216
α-helix424-4263
α-helix427-4315
Chain D: 12 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand5-7316
β-strand18-21417
α-helix92-10615
α-helix110-1156
α-helix116-1249
α-helix128-1336
α-helix169-17810
α-helix193-2019
α-helix208-2136
α-helix219-2224
α-helix223-2275
α-helix239-2402
β-strand254-256317
β-strand262-263217
α-helix266-2716
α-helix272-2765
Chain E: 22 helices, 26 β-strands
ElementResiduesLengthSheet
β-strand24118
β-strand35119
β-strand41119
β-strand44-45220
β-strand48-49220
α-helix52-6716
β-strand70121
β-strand74-79622
α-helix85-9612
β-strand102-106522
α-helix107-1104
α-helix117-12711
β-strand129-1492116
β-strand166-171616
β-strand176-181616
α-helix183-1919
β-strand198-203616
β-strand208-215816
α-helix216-2183
β-strand22417
α-helix227-2282
β-strand229-230216
α-helix231-2344
β-strand238-2481116
α-helix249-2579
α-helix265-2728
α-helix282-29716
β-strand301-305516
β-strand307-311522
α-helix313-3153
α-helix318-32811
β-strand335-340622
β-strand342123
α-helix3451
β-strand346124
α-helix3471
β-strand354124
α-helix361-3644
β-strand367-372622
α-helix377-39014
β-strand395125
α-helix397-40913
α-helix412-4176
α-helix419-42810
β-strand434125
α-helix436-44510
β-strand447126
α-helix449-4568
Chain F: 21 helices, 26 β-strands
ElementResiduesLengthSheet
β-strand20127
β-strand31128
α-helix361
β-strand37128
α-helix381
β-strand40-41229
β-strand44-45229
α-helix48-6316
β-strand66118
β-strand70-74526
α-helix81-9212
β-strand98-102526
α-helix103-1053
α-helix113-12210
β-strand125-148247
β-strand154-16187
β-strand166-17167
α-helix173-18210
β-strand188-19367
β-strand199-20467
β-strand20717
β-strand22117
α-helix223-2253
β-strand230-240117
α-helix241-2499
α-helix253-2597
α-helix267-28317
β-strand286-29057
β-strand292-296526
α-helix298-3003
α-helix303-31210
β-strand320-325626
β-strand330-331230
α-helix3321
β-strand338-339230
α-helix345-3495
β-strand351-355526
α-helix361-37414
β-strand379131
α-helix381-39313
α-helix396-41217
β-strand418131
α-helix420-42910
β-strand431132
α-helix433-44210
α-helix444-4463
β-strand448133
Chain G: 20 helices, 26 β-strands
ElementResiduesLengthSheet
β-strand24134
β-strand35135
β-strand41135
β-strand44-45236
β-strand48-49236
α-helix52-6716
β-strand70127
β-strand73-79732
α-helix85-9612
β-strand102-106532
α-helix107-1104
α-helix117-12812
β-strand130-151227
β-strand161-172127
β-strand175-18177
α-helix185-1917
β-strand198-20367
β-strand209-21577
α-helix216-2183
β-strand22418
α-helix2281
β-strand229-23027
α-helix231-2344
β-strand238-248117
α-helix249-2579
α-helix265-2728
α-helix282-29716
β-strand301-30447
β-strand307-311532
α-helix313-3153
α-helix318-32710
β-strand335-340632
β-strand342133
β-strand344-346337
α-helix3471
β-strand354-357437
α-helix361-3644
β-strand367-372632
α-helix377-39014
β-strand395138
α-helix397-40913
α-helix412-42817
β-strand434138
α-helix436-44510
β-strand447139
α-helix449-4546
Chain H: 22 helices, 27 β-strands
ElementResiduesLengthSheet
β-strand20140
β-strand31141
α-helix361
β-strand37141
α-helix381
β-strand40-41242
β-strand44-45242
α-helix48-6316
β-strand66134
β-strand70-74539
α-helix81-9212
β-strand98-102539
α-helix103-1064
α-helix113-12311
β-strand125-146228
β-strand155-16288
β-strand165-17178
α-helix173-18210
β-strand188-19368
β-strand199-20468
α-helix206-2116
β-strand214115
β-strand22118
β-strand22216
α-helix223-2253
β-strand230-240118
α-helix241-2499
α-helix253-2597
α-helix267-28317
β-strand286-29058
β-strand292-296539
α-helix298-3003
β-strand302143
α-helix303-31210
β-strand320-325639
β-strand330-331244
α-helix3321
β-strand333143
β-strand338-339244
α-helix345-3495
β-strand351-355539
α-helix361-37414
α-helix381-39313
α-helix396-41217
α-helix420-42910
β-strand431145
α-helix433-44210
α-helix444-4463
β-strand448146

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Helicase SWR1Aprotein1544Saccharomyces cerevisiae W303Q05471 (AlphaFold model)
Vacuolar protein sorting-associated protein 72Bprotein795Saccharomyces cerevisiae W303Q03388 (AlphaFold model)
Actin-like protein ARP6Cprotein438Saccharomyces cerevisiae W303Q12509 (AlphaFold model)
Vacuolar protein sorting-associated protein 71Dprotein280Saccharomyces cerevisiae W303Q03433 (AlphaFold model)
RuvB-like protein 1E, G, Iprotein837Saccharomyces cerevisiae W303Q03940
RuvB-like protein 2F, H, Jprotein471Saccharomyces cerevisiae W303Q12464
DNA (147-mer)YDNA147synthetic construct
DNA (147-mer)ZDNA147synthetic construct
Sequence of entity 1 (A), FASTA
>9B1D_1 Helicase SWR1 (chains A)
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
DEYMIRFIANGYYYGSGGSGDYKDHDGDYKDHDIDYKDDDDKGS
Sequence of entity 2 (B), FASTA
>9B1D_2 Vacuolar protein sorting-associated protein 72 (chains B)
MSDEGADKSLDTNTEFIIQTRSRRSNAGNKLQKLLEQELRDIESTKRQISSYKNGNDDEE
DEIGLLFQEDEDDEDFEMMAKDDDDEGEEKEDETQSIRKEPSQASSEQAADDLMFSSSES
EDSSNENDEDAEEKEIRRQELLSRKKRNKRLQKGPVVIKKQKPKPKSGEAIPRSHHTHEQ
LNAETLLLNTRRTSKRSSVMENTMKVYEKLSKAEKKRKIIQERIRKHKEQESQHMLTQEE
RLRIAKETEKLNILSLDKFKEQEVWKKENRLALQKRQKQKFQPNETILQFLSTAWLMTPA
MELEDRKYWQEQLNKRDKKKKKYPRKPKKNLNLGKQDASDDKKRESEESIKNDGDVNSLG
ENSSSVHNQKRIEETSTNDTVEGESSPDAAVSRVNSDELKPTALPDVTLDAIANKQSTVD
EAPNSQPQKNIITNEQKITNVGEPIQNLHNEEIKDEMVSALESRENTFENSSPAAQVVSQ
RDNSATPTPSNSTGTEDTILISPDTDIKGEPEPCLKTEGIENLSHNVPQETKSNTDVSFL
KQVTFTDHPQVAIIDTEESPSKKDTANVDESSAENSLSTQTYEGPEQLTSRNFVTLYDFP
NAPPNLKDFNTNLFGDRWSYTNGLSATQRPQDMKTVFHSILPSPPQSSVPSPTVDISLDL
SALANFPSFGEYDKKIVHQINTEINKDLEIKIKTQPPTGVFLANGIRKKCLITNKECQYF
DPRTGVPYSDVEAYKIIQRIQDPISKEEGRSDIKRDETTNEDSDDQVRFKWFGFKNGGIY
LDLSQRPAKGVPEGF
Sequence of entity 3 (C), FASTA
>9B1D_3 Actin-like protein ARP6 (chains C)
METPPIVIDNGSYEIKFGPSTNKKPFRALNALAKDKFGTSYLSNHIKNIKDISSITFRRP
HELGQLTLWELESCIWDYCLFNPSEFDGFDLKEGKGHHLVASESCMTLPELSKHADQVIF
EEYEFDSLFKSPVAVFVPFTKSYKGEMRTISGKDEDIDIVRGNSDSTNSTSSESKNAQDS
GSDYHDFQLVIDSGFNCTWIIPVLKGIPYYKAVKKLDIGGRFLTGLLKETLSFRHYNMMD
ETILVNNIKEQCLFVSPVSYFDSFKTKDKHALEYVLPDFQTSFLGYVRNPRKENVPLPED
AQIITLTDELFTIPETFFHPEISQITKPGIVEAILESLSMLPEIVRPLMVGNIVCTGGNF
NLPNFAQRLAAELQRQLPTDWTCHVSVPEGDCALFGWEVMSQFAKTDSYRKARVTREEYY
EHGPDWCTKHRFGYQNWI
Sequence of entity 4 (D), FASTA
>9B1D_4 Vacuolar protein sorting-associated protein 71 (chains D)
MKALVEEIDKKTYNPDIYFTSLDPQARRYTSKKINKQGTISTSRPVKRINYSLADLEARL
YTSRSEGDGNSISRQDDRNSKNSHSFEERYTQQEILQSDRRFMELNTENFSDLPNVPTLL
SDLTGVPRDRIESTTKPISQTSDGLSALMGGSSFVKEHSKYGHGWVLKPETLREIQLSYK
STKLPKPKRKNTNRIVALKKVLSSKRNLHSFLDSALLNLMDKNVIYHNVYNKRYFKVLPL
ITTCSICGGYDSISSCVNCGNKICSVSCFKLHNETRCRNR
Sequence of entity 5 (E, G, I), FASTA
>9B1D_5 RuvB-like protein 1 (chains E, G, I)
MVAISEVKENPGVNSSNSGAVTRTAAHTHIKGLGLDESGVAKRVEGGFVGQIEAREACGV
IVDLIKAKKMSGRAILLAGGPSTGKTALALAISQELGPKVPFCPLVGSELYSVEVKKTET
LMENFRRAIGLRIKETKEVYEGEVTELTPEDAENPLGGYGKTISHVIVGLKSAKGTKTLR
LDPTIYESIQREKVSIGDVIYIEANTGAVKRVGRSDAYATEFDLETEEYVPLPKGEVHKK
KEIVQDVTLHDLDVANARPQGGQDVISMMGQLLKPKKTEITEKLRQEVNKVVAKYIDQGV
AELIPGVLFIDEVNMLDIEIFTYLNKALESNIAPVVVLASNRGMTTVRGTEDVISPHGVP
PDLIDRLLIVRTLPYDKDEIRTIIERRATVERLQVESSALDLLATMGTETSLRYALQLLA
PCGILAQTSNRKEIVVNDVNEAKLLFLDAKRSTKILETSANYLSGGGASMKIEEGKLVIW
INGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGY
AQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWE
EIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKA
GLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTF
KGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEE
LAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTN
Sequence of entity 6 (F, H, J), FASTA
>9B1D_6 RuvB-like protein 2 (chains F, H, J)
MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKM
VQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQA
FRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLT
KEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS
LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHM
LDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYN
EQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEV
EDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAKSADPDAMDTTE
Sequence of entity 7 (Y), FASTA
>9B1D_7 DNA (147-MER) (chains Y)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGCAAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT
Sequence of entity 8 (Z), FASTA
>9B1D_8 DNA (147-MER) (chains Z)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTTGCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Ligands and cofactors

IDNameFormulaCopies
AGSPhosphothiophosphoric acid-adenylate esterC10 H16 N5 O12 P3 S4
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P24
ZNZinc ionZn2
MGMagnesium ionMg8

Primary citation

Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler. Louder, R.K., Park, G., Ye, Z. et al. Cell (2024) 187:6849-6864.e18. DOI 10.1016/j.cell.2024.09.007 · PubMed

Other PDB entries of the same protein (UniProt Q05471 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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