Cryo-EM structure of native SWR1 bound to DNA (composite structure)

2024-12-11 REL RCSB RCSB RCSB 2024-03-13 2024-10-09 2024-10-09 2024-12-11 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM149291 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM125831 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) F32GM133151 United States Cryo-EM structure of native SWR1 bound to DNA (composite structure) Louder RK Park G Wu C Chromatin Remodeler, Snf2 family ATPase, histone exchange, H2A.Z, GENE REGULATION Louder RK Park G Ye Z Cha JS Gardner AM Lei Q Ranjan A Hollmuller E Stengel F Pugh BF Wu C Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler. Cell 187 6849 6864.e18 2024 39357520 doi:10.1016/j.cell.2024.09.007 1097-4172 EMD-44106 consensus EM volume EMD-44107 focused EM volume EMD-44108 focused EM volume EMD-44109 focused EM volume EMD-44110 other EM volume

Unmasked refinement of the same structure

9b1d FULLOVERLAP Native SWR1 bound to DNA. Native SWR1 bound to DNA. 0 1 2 3 4 5 6 7 8

Endogenously purified yeast SWR1 complex bound to 147-bp dsDNA fragment in the presence of ATPgS.

Saccharomyces cerevisiae W303 1.19 Native SWR1 complex 1 1 2 3 4 5 6

Endogenously purified yeast SWR1 complex

Saccharomyces cerevisiae W303 Helicase SWR1 Saccharomyces cerevisiae W303 0.178058172

Fusion protein with C-terminal 3xFLAG

1 LEVO MTTSRKSHAKDKKAGGEQDLADLKFRYDLLTNELFHLREFVSLVDYDPTHFNDSESFQKFLRETHLSLEERGEKFTDDVA KKGTNGDLTRRRRNLRTSTVVSSETTNEKKGDIELKLESIAPLVRNKCEELKYKLSDHSNRKSIVPQKRPIQHLKKREAA KSLKFKSERKENPLPLHEHIAEERYDHIAKVEEPSEAFTIKCPSDDSSFENTSEHYSDNFYFTTSSEEEDIKKKRGRKKK KPRIKLVVHPPKQTITNPLHVVKPGYESLHEYIASFKSLEDDLTLEEYNKYIDEQRRLLSRLKKGIENGALKYDKETDSL QPITSKEIKTIITYKPDPISYFYKQQDLQIHTDHLINQGIHMSKLFRSSTKARIARAKKVSQMIEQHFKHVAGAEERKAK EEERHKKSLARFAVQAVKKRWNMAEKAYRILRKDEEEQLKRIEGKQHLSKMLEKSTQLLEAQLNQVNDDGRSSTPSSDSN DVLSESDDDMDDELSTSSDEDEEVDADVGLENSPASTEATPTDESLNLIQLKEKYGHFNGSSTVYDSRNKDEKFPTLDKH ESSSSESSVMTGEESSIYSSSENESQNENDRESDDKTPSVGLSALFGKGEESDGDLDLDDSEDFTVNSSSVEGEELEKDQ VDNSAATFERAGDFVHTQNENRDDIKDVEEDAETKVQEEQLSVVDVPVPSLLRGNLRTYQKQGLNWLASLYNNHTNGILA DEMGLGKTIQTISLLAYLACEKENWGPHLIVVPTSVLLNWEMEFKRFAPGFKVLTYYGSPQQRKEKRKGWNKPDAFHVCI VSYQLVVQDQHSFKRKRWQYMVLDEAHNIKNFRSTRWQALLNFNTQRRLLLTGTPLQNNLAELWSLLYFLMPQTVIDGKK VSGFADLDAFQQWFGRPVDKIIETGQNFGQDKETKKTVAKLHQVLRPYLLRRLKADVEKQMPAKYEHIVYCKLSKRQRFL YDDFMSRAQTKATLASGNFMSIVNCLMQLRKVCNHPNLFEVRPILTSFVLEHCVASDYKDVERTLLKLFKKNNQVNRVDL DFLNLVFTLNDKDLTSYHAEEISKLTCVKNFVEEVNKLRETNKQLQEEFGEASFLNFQDANQYFKYSNKQKLEGTVDMLN FLKMVNKLRCDRRPIFGKNLIDLLTKDRRVKYDKSSIIDNELIKPLQTRVLDNRKIIDTFAVLTPSAVSLDMRKLALGLN DDSSVGENTRLKVMQNCFEVSNPLHQLQTKLTIAFPDKSLLQYDCGKLQKLAILLQQLKDNGHRALIFTQMTKVLDVLEQ FLNYHGYLYMRLDGATKIEDRQILTERFNTDSRITVFILSSRSGGLGINLTGADTVIFYDSDWNPAMDKQCQDRCHRIGQ TRDVHIYRFVSEHTIESNILKKANQKRQLDNVVIQEGDFTTDYFSKLSVRDLLGSELPENASGGDKPLIADADVAAKDPR QLERLLAQAEDEDDVKAANLAMREVEIDNDDFDESTEKKAANEEEENHAELDEYEGTAHVDEYMIRFIANGYYYGSGGSG DYKDHDGDYKDHDIDYKDDDDKGS 3.6.4.12 Vacuolar protein sorting-associated protein 72 Saccharomyces cerevisiae W303 0.090709008 1 LEVO MSDEGADKSLDTNTEFIIQTRSRRSNAGNKLQKLLEQELRDIESTKRQISSYKNGNDDEEDEIGLLFQEDEDDEDFEMMA KDDDDEGEEKEDETQSIRKEPSQASSEQAADDLMFSSSESEDSSNENDEDAEEKEIRRQELLSRKKRNKRLQKGPVVIKK QKPKPKSGEAIPRSHHTHEQLNAETLLLNTRRTSKRSSVMENTMKVYEKLSKAEKKRKIIQERIRKHKEQESQHMLTQEE RLRIAKETEKLNILSLDKFKEQEVWKKENRLALQKRQKQKFQPNETILQFLSTAWLMTPAMELEDRKYWQEQLNKRDKKK KKYPRKPKKNLNLGKQDASDDKKRESEESIKNDGDVNSLGENSSSVHNQKRIEETSTNDTVEGESSPDAAVSRVNSDELK PTALPDVTLDAIANKQSTVDEAPNSQPQKNIITNEQKITNVGEPIQNLHNEEIKDEMVSALESRENTFENSSPAAQVVSQ RDNSATPTPSNSTGTEDTILISPDTDIKGEPEPCLKTEGIENLSHNVPQETKSNTDVSFLKQVTFTDHPQVAIIDTEESP SKKDTANVDESSAENSLSTQTYEGPEQLTSRNFVTLYDFPNAPPNLKDFNTNLFGDRWSYTNGLSATQRPQDMKTVFHSI LPSPPQSSVPSPTVDISLDLSALANFPSFGEYDKKIVHQINTEINKDLEIKIKTQPPTGVFLANGIRKKCLITNKECQYF DPRTGVPYSDVEAYKIIQRIQDPISKEEGRSDIKRDETTNEDSDDQVRFKWFGFKNGGIYLDLSQRPAKGVPEGF Q03388 Actin-like protein ARP6 Saccharomyces cerevisiae W303 0.050100582 1 LEVO METPPIVIDNGSYEIKFGPSTNKKPFRALNALAKDKFGTSYLSNHIKNIKDISSITFRRPHELGQLTLWELESCIWDYCL FNPSEFDGFDLKEGKGHHLVASESCMTLPELSKHADQVIFEEYEFDSLFKSPVAVFVPFTKSYKGEMRTISGKDEDIDIV RGNSDSTNSTSSESKNAQDSGSDYHDFQLVIDSGFNCTWIIPVLKGIPYYKAVKKLDIGGRFLTGLLKETLSFRHYNMMD ETILVNNIKEQCLFVSPVSYFDSFKTKDKHALEYVLPDFQTSFLGYVRNPRKENVPLPEDAQIITLTDELFTIPETFFHP EISQITKPGIVEAILESLSMLPEIVRPLMVGNIVCTGGNFNLPNFAQRLAAELQRQLPTDWTCHVSVPEGDCALFGWEVM SQFAKTDSYRKARVTREEYYEHGPDWCTKHRFGYQNWI Q12509 Vacuolar protein sorting-associated protein 71 Saccharomyces cerevisiae W303 0.032073478999999995 1 LEVO MKALVEEIDKKTYNPDIYFTSLDPQARRYTSKKINKQGTISTSRPVKRINYSLADLEARLYTSRSEGDGNSISRQDDRNS KNSHSFEERYTQQEILQSDRRFMELNTENFSDLPNVPTLLSDLTGVPRDRIESTTKPISQTSDGLSALMGGSSFVKEHSK YGHGWVLKPETLREIQLSYKSTKLPKPKRKNTNRIVALKKVLSSKRNLHSFLDSALLNLMDKNVIYHNVYNKRYFKVLPL ITTCSICGGYDSISSCVNCGNKICSVSCFKLHNETRCRNR Q03433 RuvB-like protein 1 Saccharomyces cerevisiae W303 0.09141324199999999

Fusion protein with C-terminal maltose-binding protein

3 LEVO MVAISEVKENPGVNSSNSGAVTRTAAHTHIKGLGLDESGVAKRVEGGFVGQIEAREACGVIVDLIKAKKMSGRAILLAGG PSTGKTALALAISQELGPKVPFCPLVGSELYSVEVKKTETLMENFRRAIGLRIKETKEVYEGEVTELTPEDAENPLGGYG KTISHVIVGLKSAKGTKTLRLDPTIYESIQREKVSIGDVIYIEANTGAVKRVGRSDAYATEFDLETEEYVPLPKGEVHKK KEIVQDVTLHDLDVANARPQGGQDVISMMGQLLKPKKTEITEKLRQEVNKVVAKYIDQGVAELIPGVLFIDEVNMLDIEI FTYLNKALESNIAPVVVLASNRGMTTVRGTEDVISPHGVPPDLIDRLLIVRTLPYDKDEIRTIIERRATVERLQVESSAL DLLATMGTETSLRYALQLLAPCGILAQTSNRKEIVVNDVNEAKLLFLDAKRSTKILETSANYLSGGGASMKIEEGKLVIW INGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLY PFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFK YENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTF KGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIM PNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTN 3.6.4.12 RuvB-like protein 2 Saccharomyces cerevisiae W303 0.051673488 3 LEVO MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKMVQNGTIAGRAVLVAGPPSTG KTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQAFRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTI KTTDMETIYELGNKMIDGLTKEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHMLDIECFSFINRALEDEFAPI VMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYNEQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSS NLISVAQQIAMKRKNNTVEVEDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAKSADPDAMDTTE Q12464 3.6.4.12 DNA (147-MER) synthetic construct 0.045145753999999996 1 (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DC)(DA)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC)(DC)(DT)(DG)(DT) DNA DNA (147-MER) synthetic construct 0.045604046999999995 1 (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DT)(DG)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DC)(DA)(DG) DNA PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER 0.0005232469999999999 4 AGS MAGNESIUM ION 2.4305e-05 8 MG ZINC ION 6.5409e-05 2 ZN ADENOSINE-5'-DIPHOSPHATE 0.000427201 4 ADP singleParticle particle 0.125 7.6 20.0 HEPES 0.2 EDTA 2.0 MgCl2 magnesium chloride 100.0 NaCl sodium chloride 0.01 IGEPAL CA-630 3.5 glycerol 0.25 TCEP 1.0 ATP-gamma-s 0.05 glutaraldehyde

20 mM HEPES pH 7.6, 0.2 mM EDTA, 2 mM MgCl2, 100 mM NaCl, 0.01% IGEPAL CA-630, 3.5% glycerol, and 0.25 mM TCEP, 1 mM ATP-gamma-s, 0.05% glutaraldehyde.

Quantifoil R2/1 COPPER 400 GRAPHENE OXIDE CONTINUOUS PLASMA CLEANING 90 AIR ETHANE 100 277 FEI VITROBOT MARK IV

6 second blot time and blot force of 12..

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 2.0 3.6 48543.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN SerialEM 3.7.6 GATAN K3 (6k x 4k) 1 5379 4.0 54.0

Each micrograph was fractionated into 64 frames within a 4 second exposure.

1 386667

2D classification was used to remove graphene edges.

EMD-4395 1 C1 FOURIER SPACE 3.3 FSC 0.143 CUT-OFF RELION 3.1.3

Refined maps were post-processed using DeepEMhancer

101246 MAXIMUM LIKELIHOOD RELION 3.1.3 MAXIMUM LIKELIHOOD RELION 3.1.3 RELION 3.1.3 emd_44074.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 395.52 395.52 395.52 90.0 90.0 90.0 X Y Z -0.039235763 1.9881451 0.0012745858 0.025840033 1.03 1.03 1.03 0.15 AUTHOR ::::EMDATABANK.org::::EMD-44074:::: Composite cryo-EM map of SWR1-DNA complex. 6GEJ PDB experimental model AlphaFold in silico model FLEXIBLE FIT ISOLDE 1.7 Cross-correlation coefficient REAL 84.0