EMDB-44074: Cryo-EM structure of native SWR1 bound to DNA (composite structure)

Basic information

Entry

Database: EMDB / ID: EMD-44074

• Title: Cryo-EM structure of native SWR1 bound to DNA (composite structure)
• Map data: Composite cryo-EM map of SWR1-DNA complex.

Sample

• Complex: Native SWR1 bound to DNA.
  • Complex: Native SWR1 complex
    • Protein or peptide: x 6 types
  • DNA: x 2 types
• Ligand: x 4 types

• Keywords: Chromatin Remodeler / Snf2 family ATPase / histone exchange / H2A.Z / GENE REGULATION

Function / homology

Function:

TTT Hsp90 cochaperone complex / R2TP complex / Swr1 complex / protein targeting to vacuole / Ino80 complex / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / DNA helicase activity / nucleosome binding / nuclear periphery / rRNA processing / 5'-3' DNA helicase activity / DNA helicase / histone binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / protein stabilization / chromatin remodeling / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / ATP hydrolysis activity / zinc ion binding / ATP binding / nucleus / cytoplasm

Domain/homology:

Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Zinc finger, HIT-type / Vps72/YL1, N-terminal / YL1 nuclear protein / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / Actin / Actin family / Actin / ATPase, nucleotide binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase

Component:

Vacuolar protein sorting-associated protein 72 / Vacuolar protein sorting-associated protein 71 / RuvB-like protein 2 / Actin-like protein ARP6

• Biological species: Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae W303 (yeast) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 3.3 Å
• Authors: Louder RK / Park G / Wu C

Funding support

United States, 3 items

Organization	Grant number	Country
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

• Citation: Journal: Cell / Year: 2024; Title: Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler.; Authors: Robert K Louder / Giho Park / Ziyang Ye / Justin S Cha / Anne M Gardner / Qin Lei / Anand Ranjan / Eva Höllmüller / Florian Stengel / B Franklin Pugh / Carl Wu / ; Abstract: The SWR1 chromatin remodeling complex is recruited to +1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. Here, we use cryoelectron microscopy (cryo-EM) to resolve the structural basis of the SWR1 interaction with free DNA, revealing a distinct open conformation of the Swr1 ATPase that enables sliding from accessible DNA to nucleosomes. A complete structural model of the SWR1-nucleosome complex illustrates critical roles for Swc2 and Swc3 subunits in oriented nucleosome engagement by SWR1. Moreover, an extended DNA-binding α helix within the Swc3 subunit enables sensing of nucleosome linker length and is essential for SWR1-promoter-specific recruitment and activity. The previously unresolved N-SWR1 subcomplex forms a flexible extended structure, enabling multivalent recognition of acetylated histone tails by reader domains to further direct SWR1 toward the +1 nucleosome. Altogether, our findings provide a generalizable mechanism for promoter-specific targeting of chromatin and transcription complexes.

History

Deposition	Mar 13, 2024	-
Header (metadata) release	Oct 9, 2024	-
Map release	Oct 9, 2024	-
Update	Dec 11, 2024	-
Current status	Dec 11, 2024	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_44074.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Composite cryo-EM map of SWR1-DNA complex.
• Voxel size: X=Y=Z: 1.03 Å

Density

Contour Level	By AUTHOR: 0.15
Minimum - Maximum	-0.039235763 - 1.9881451
Average (Standard dev.)	0.0012745858 (±0.025840033)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 384 384 384 Spacing 384 384 384
Cell	A=B=C: 395.52 Å α=β=γ: 90.0 °

Supplemental data

Sample components

Entire : Native SWR1 bound to DNA.

• Entire: Name: Native SWR1 bound to DNA.

Components

• Complex: Native SWR1 bound to DNA.
  • Complex: Native SWR1 complex
    • Protein or peptide: Helicase SWR1
    • Protein or peptide: Vacuolar protein sorting-associated protein 72
    • Protein or peptide: Actin-like protein ARP6
    • Protein or peptide: Vacuolar protein sorting-associated protein 71
    • Protein or peptide: RuvB-like protein 1
    • Protein or peptide: RuvB-like protein 2
  • DNA: DNA (147-MER)
  • DNA: DNA (147-MER)
• Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
• Ligand: MAGNESIUM ION
• Ligand: ZINC ION
• Ligand: ADENOSINE-5'-DIPHOSPHATE

Supramolecule #1: Native SWR1 bound to DNA.

• Supramolecule: Name: Native SWR1 bound to DNA. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8; Details: Endogenously purified yeast SWR1 complex bound to 147-bp dsDNA fragment in the presence of ATPgS.
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303
• Molecular weight: Theoretical: 1.19 MDa

Supramolecule #2: Native SWR1 complex

• Supramolecule: Name: Native SWR1 complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6 / Details: Endogenously purified yeast SWR1 complex
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

Macromolecule #1: Helicase SWR1

• Macromolecule: Name: Helicase SWR1 / type: protein_or_peptide / ID: 1 / Details: Fusion protein with C-terminal 3xFLAG / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
• Source (natural): Organism: Saccharomyces cerevisiae W303 (yeast)
• Molecular weight: Theoretical: 178.058172 KDa

Sequence

String:

MTTSRKSHAK DKKAGGEQDL ADLKFRYDLL TNELFHLREF VSLVDYDPTH FNDSESFQKF LRETHLSLEE RGEKFTDDVA KKGTNGDLT RRRRNLRTST VVSSETTNEK KGDIELKLES IAPLVRNKCE ELKYKLSDHS NRKSIVPQKR PIQHLKKREA A KSLKFKSE RKENPLPLHE HIAEERYDHI AKVEEPSEAF TIKCPSDDSS FENTSEHYSD NFYFTTSSEE EDIKKKRGRK KK KPRIKLV VHPPKQTITN PLHVVKPGYE SLHEYIASFK SLEDDLTLEE YNKYIDEQRR LLSRLKKGIE NGALKYDKET DSL QPITSK EIKTIITYKP DPISYFYKQQ DLQIHTDHLI NQGIHMSKLF RSSTKARIAR AKKVSQMIEQ HFKHVAGAEE RKAK EEERH KKSLARFAVQ AVKKRWNMAE KAYRILRKDE EEQLKRIEGK QHLSKMLEKS TQLLEAQLNQ VNDDGRSSTP SSDSN DVLS ESDDDMDDEL STSSDEDEEV DADVGLENSP ASTEATPTDE SLNLIQLKEK YGHFNGSSTV YDSRNKDEKF PTLDKH ESS SSESSVMTGE ESSIYSSSEN ESQNENDRES DDKTPSVGLS ALFGKGEESD GDLDLDDSED FTVNSSSVEG EELEKDQ VD NSAATFERAG DFVHTQNENR DDIKDVEEDA ETKVQEEQLS VVDVPVPSLL RGNLRTYQKQ GLNWLASLYN NHTNGILA D EMGLGKTIQT ISLLAYLACE KENWGPHLIV VPTSVLLNWE MEFKRFAPGF KVLTYYGSPQ QRKEKRKGWN KPDAFHVCI VSYQLVVQDQ HSFKRKRWQY MVLDEAHNIK NFRSTRWQAL LNFNTQRRLL LTGTPLQNNL AELWSLLYFL MPQTVIDGKK VSGFADLDA FQQWFGRPVD KIIETGQNFG QDKETKKTVA KLHQVLRPYL LRRLKADVEK QMPAKYEHIV YCKLSKRQRF L YDDFMSRA QTKATLASGN FMSIVNCLMQ LRKVCNHPNL FEVRPILTSF VLEHCVASDY KDVERTLLKL FKKNNQVNRV DL DFLNLVF TLNDKDLTSY HAEEISKLTC VKNFVEEVNK LRETNKQLQE EFGEASFLNF QDANQYFKYS NKQKLEGTVD MLN FLKMVN KLRCDRRPIF GKNLIDLLTK DRRVKYDKSS IIDNELIKPL QTRVLDNRKI IDTFAVLTPS AVSLDMRKLA LGLN DDSSV GENTRLKVMQ NCFEVSNPLH QLQTKLTIAF PDKSLLQYDC GKLQKLAILL QQLKDNGHRA LIFTQMTKVL DVLEQ FLNY HGYLYMRLDG ATKIEDRQIL TERFNTDSRI TVFILSSRSG GLGINLTGAD TVIFYDSDWN PAMDKQCQDR CHRIGQ TRD VHIYRFVSEH TIESNILKKA NQKRQLDNVV IQEGDFTTDY FSKLSVRDLL GSELPENASG GDKPLIADAD VAAKDPR QL ERLLAQAEDE DDVKAANLAM REVEIDNDDF DESTEKKAAN EEEENHAELD EYEGTAHVDE YMIRFIANGY YYGSGGSG D YKDHDGDYKD HDIDYKDDDD KGS

Macromolecule #2: Vacuolar protein sorting-associated protein 72

• Macromolecule: Name: Vacuolar protein sorting-associated protein 72 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae W303 (yeast)
• Molecular weight: Theoretical: 90.709008 KDa

Sequence

String:

MSDEGADKSL DTNTEFIIQT RSRRSNAGNK LQKLLEQELR DIESTKRQIS SYKNGNDDEE DEIGLLFQED EDDEDFEMMA KDDDDEGEE KEDETQSIRK EPSQASSEQA ADDLMFSSSE SEDSSNENDE DAEEKEIRRQ ELLSRKKRNK RLQKGPVVIK K QKPKPKSG EAIPRSHHTH EQLNAETLLL NTRRTSKRSS VMENTMKVYE KLSKAEKKRK IIQERIRKHK EQESQHMLTQ EE RLRIAKE TEKLNILSLD KFKEQEVWKK ENRLALQKRQ KQKFQPNETI LQFLSTAWLM TPAMELEDRK YWQEQLNKRD KKK KKYPRK PKKNLNLGKQ DASDDKKRES EESIKNDGDV NSLGENSSSV HNQKRIEETS TNDTVEGESS PDAAVSRVNS DELK PTALP DVTLDAIANK QSTVDEAPNS QPQKNIITNE QKITNVGEPI QNLHNEEIKD EMVSALESRE NTFENSSPAA QVVSQ RDNS ATPTPSNSTG TEDTILISPD TDIKGEPEPC LKTEGIENLS HNVPQETKSN TDVSFLKQVT FTDHPQVAII DTEESP SKK DTANVDESSA ENSLSTQTYE GPEQLTSRNF VTLYDFPNAP PNLKDFNTNL FGDRWSYTNG LSATQRPQDM KTVFHSI LP SPPQSSVPSP TVDISLDLSA LANFPSFGEY DKKIVHQINT EINKDLEIKI KTQPPTGVFL ANGIRKKCLI TNKECQYF D PRTGVPYSDV EAYKIIQRIQ DPISKEEGRS DIKRDETTNE DSDDQVRFKW FGFKNGGIYL DLSQRPAKGV PEGF

UniProtKB: Vacuolar protein sorting-associated protein 72

Macromolecule #3: Actin-like protein ARP6

• Macromolecule: Name: Actin-like protein ARP6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae W303 (yeast)
• Molecular weight: Theoretical: 50.100582 KDa

Sequence

String:

METPPIVIDN GSYEIKFGPS TNKKPFRALN ALAKDKFGTS YLSNHIKNIK DISSITFRRP HELGQLTLWE LESCIWDYCL FNPSEFDGF DLKEGKGHHL VASESCMTLP ELSKHADQVI FEEYEFDSLF KSPVAVFVPF TKSYKGEMRT ISGKDEDIDI V RGNSDSTN STSSESKNAQ DSGSDYHDFQ LVIDSGFNCT WIIPVLKGIP YYKAVKKLDI GGRFLTGLLK ETLSFRHYNM MD ETILVNN IKEQCLFVSP VSYFDSFKTK DKHALEYVLP DFQTSFLGYV RNPRKENVPL PEDAQIITLT DELFTIPETF FHP EISQIT KPGIVEAILE SLSMLPEIVR PLMVGNIVCT GGNFNLPNFA QRLAAELQRQ LPTDWTCHVS VPEGDCALFG WEVM SQFAK TDSYRKARVT REEYYEHGPD WCTKHRFGYQ NWI

UniProtKB: Actin-like protein ARP6

Macromolecule #4: Vacuolar protein sorting-associated protein 71

• Macromolecule: Name: Vacuolar protein sorting-associated protein 71 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae W303 (yeast)
• Molecular weight: Theoretical: 32.073479 KDa

Sequence

String:

MKALVEEIDK KTYNPDIYFT SLDPQARRYT SKKINKQGTI STSRPVKRIN YSLADLEARL YTSRSEGDGN SISRQDDRNS KNSHSFEER YTQQEILQSD RRFMELNTEN FSDLPNVPTL LSDLTGVPRD RIESTTKPIS QTSDGLSALM GGSSFVKEHS K YGHGWVLK PETLREIQLS YKSTKLPKPK RKNTNRIVAL KKVLSSKRNL HSFLDSALLN LMDKNVIYHN VYNKRYFKVL PL ITTCSIC GGYDSISSCV NCGNKICSVS CFKLHNETRC RNR

UniProtKB: Vacuolar protein sorting-associated protein 71

Macromolecule #5: RuvB-like protein 1

• Macromolecule: Name: RuvB-like protein 1 / type: protein_or_peptide / ID: 5 ; Details: Fusion protein with C-terminal maltose-binding protein; Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
• Source (natural): Organism: Saccharomyces cerevisiae W303 (yeast)
• Molecular weight: Theoretical: 91.413242 KDa

Sequence

String:

MVAISEVKEN PGVNSSNSGA VTRTAAHTHI KGLGLDESGV AKRVEGGFVG QIEAREACGV IVDLIKAKKM SGRAILLAGG PSTGKTALA LAISQELGPK VPFCPLVGSE LYSVEVKKTE TLMENFRRAI GLRIKETKEV YEGEVTELTP EDAENPLGGY G KTISHVIV GLKSAKGTKT LRLDPTIYES IQREKVSIGD VIYIEANTGA VKRVGRSDAY ATEFDLETEE YVPLPKGEVH KK KEIVQDV TLHDLDVANA RPQGGQDVIS MMGQLLKPKK TEITEKLRQE VNKVVAKYID QGVAELIPGV LFIDEVNMLD IEI FTYLNK ALESNIAPVV VLASNRGMTT VRGTEDVISP HGVPPDLIDR LLIVRTLPYD KDEIRTIIER RATVERLQVE SSAL DLLAT MGTETSLRYA LQLLAPCGIL AQTSNRKEIV VNDVNEAKLL FLDAKRSTKI LETSANYLSG GGASMKIEEG KLVIW INGD KGYNGLAEVG KKFEKDTGIK VTVEHPDKLE EKFPQVAATG DGPDIIFWAH DRFGGYAQSG LLAEITPDKA FQDKLY PFT WDAVRYNGKL IAYPIAVEAL SLIYNKDLLP NPPKTWEEIP ALDKELKAKG KSALMFNLQE PYFTWPLIAA DGGYAFK YE NGKYDIKDVG VDNAGAKAGL TFLVDLIKNK HMNADTDYSI AEAAFNKGET AMTINGPWAW SNIDTSKVNY GVTVLPTF K GQPSKPFVGV LSAGINAASP NKELAKEFLE NYLLTDEGLE AVNKDKPLGA VALKSYEEEL AKDPRIAATM ENAQKGEIM PNIPQMSAFW YAVRTAVINA ASGRQTVDEA LKDAQTN

Macromolecule #6: RuvB-like protein 2

• Macromolecule: Name: RuvB-like protein 2 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
• Source (natural): Organism: Saccharomyces cerevisiae W303 (yeast)
• Molecular weight: Theoretical: 51.673488 KDa

Sequence

String:

MSIQTSDPNE TSDLKSLSLI AAHSHITGLG LDENLQPRPT SEGMVGQLQA RRAAGVILKM VQNGTIAGRA VLVAGPPSTG KTALAMGVS QSLGKDVPFT AIAGSEIFSL ELSKTEALTQ AFRKSIGIKI KEETELIEGE VVEIQIDRSI TGGHKQGKLT I KTTDMETI YELGNKMIDG LTKEKVLAGD VISIDKASGK ITKLGRSFAR SRDYDAMGAD TRFVQCPEGE LQKRKTVVHT VS LHEIDVI NSRTQGFLAL FTGDTGEIRS EVRDQINTKV AEWKEEGKAE IVPGVLFIDE VHMLDIECFS FINRALEDEF API VMMATN RGVSKTRGTN YKSPHGLPLD LLDRSIIITT KSYNEQEIKT ILSIRAQEEE VELSSDALDL LTKTGVETSL RYSS NLISV AQQIAMKRKN NTVEVEDVKR AYLLFLDSAR SVKYVQENES QYIDDQGNVQ ISIAKSADPD AMDTTE

UniProtKB: RuvB-like protein 2

Macromolecule #7: DNA (147-MER)

• Macromolecule: Name: DNA (147-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 45.145754 KDa

Sequence

String:

(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)

Macromolecule #8: DNA (147-MER)

• Macromolecule: Name: DNA (147-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 45.604047 KDa

Sequence

String:

(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)

Macromolecule #9: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

• Macromolecule: Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 9 / Number of copies: 4 / Formula: AGS
• Molecular weight: Theoretical: 523.247 Da

Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

Macromolecule #10: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 8 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #11: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 4 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.125 mg/mL

Buffer

pH: 7.6
Component:

Concentration	Name	Formula
20.0 mM	HEPES
0.2 mM	EDTA
2.0 mM	magnesium chloride	MgCl2
100.0 mM	sodium chloride	NaCl
0.01 %	IGEPAL CA-630
3.5 %	glycerol
0.25 mM	TCEP
1.0 mM	ATP-gamma-s
0.05 %	glutaraldehyde

Details: 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.

• Grid: Model: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 6 second blot time and blot force of 12..

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Software: Name: SerialEM (ver. 3.7.6)
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5379 / Average exposure time: 4.0 sec. / Average electron dose: 54.0 e/Ų; Details: Each micrograph was fractionated into 64 frames within a 4 second exposure.
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 70.0 µm / Calibrated magnification: 48543 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 2.0 µm
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 386667 ; Details: 2D classification was used to remove graphene edges.

Startup model

Type of model: EMDB MAP
EMDB ID:

4395

• Final reconstruction: Number classes used: 1 / Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3); Details: Refined maps were post-processed using DeepEMhancer; Number images used: 101246
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
• Final 3D classification: Software - Name: RELION (ver. 3.1.3)

Atomic model buiding 1

Initial model

PDB ID	Chain
6gej	source_name: PDB, initial_model_type: experimental model
	source_name: AlphaFold, initial_model_type: in silico model

• Software: Name: ISOLDE (ver. 1.7)
• Refinement: Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 84 / Target criteria: Cross-correlation coefficient

Output model

PDB-9b1d:
Cryo-EM structure of native SWR1 bound to DNA (composite structure)