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- PDB-9b1e: Cryo-EM structure of native SWR1 bound to nucleosome (composite s... -

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Basic information

Entry
Database: PDB / ID: 9b1e
TitleCryo-EM structure of native SWR1 bound to nucleosome (composite structure)
Components
  • (DNA (214-MER)) x 2
  • (RuvB-like protein ...) x 2
  • (Vacuolar protein sorting-associated protein ...) x 2
  • Actin-like protein ARP6
  • Helicase SWR1
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • SWR1-complex protein 3
KeywordsGENE REGULATION / Chromatin Remodeler / Snf2 family ATPase / histone exchange / H2A.Z
Function / homology
Function and homology information


Interleukin-7 signaling / Chromatin modifying enzymes / Factors involved in megakaryocyte development and platelet production / RCAF complex / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones ...Interleukin-7 signaling / Chromatin modifying enzymes / Factors involved in megakaryocyte development and platelet production / RCAF complex / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / ATP-dependent H2AZ histone chaperone activity / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / TTT Hsp90 cochaperone complex / polytene chromosome / R2TP complex / Swr1 complex / protein targeting to vacuole / Ino80 complex / box C/D snoRNP assembly / endoplasmic reticulum organization / 3'-5' DNA helicase activity / nucleosomal DNA binding / NuA4 histone acetyltransferase complex / DNA helicase activity / nucleosome binding / nuclear periphery / rRNA processing / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / 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 / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
SWR1-complex protein 3 / 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 ...SWR1-complex protein 3 / 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 / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / ATPase, nucleotide binding domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H4 / Histone H2B / Histone H2A / Histone H3 / SWR1-complex protein 3 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H4 / Histone H2B / Histone H2A / Histone H3 / SWR1-complex protein 3 / Vacuolar protein sorting-associated protein 72 / Vacuolar protein sorting-associated protein 71 / RuvB-like protein 2 / Actin-like protein ARP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Drosophila melanogaster (fruit fly)
Saccharomyces cerevisiae W303 (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsLouder, R.K. / Park, G. / Wu, C.
Funding support United States, 3items
OrganizationGrant numberCountry
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
CitationJournal: 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. ...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
DepositionMar 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Dec 11, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helicase SWR1
B: Vacuolar protein sorting-associated protein 72
C: Actin-like protein ARP6
D: Vacuolar protein sorting-associated protein 71
E: RuvB-like protein 1
F: RuvB-like protein 2
G: RuvB-like protein 1
H: RuvB-like protein 2
I: RuvB-like protein 1
J: RuvB-like protein 2
K: SWR1-complex protein 3
Q: Histone H2A
R: Histone H2B
S: Histone H2A
T: Histone H2B
U: Histone H3
V: Histone H4
W: Histone H3
X: Histone H4
Y: DNA (214-MER)
Z: DNA (214-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,099,12241
Polymers1,095,24721
Non-polymers3,87520
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 7 types, 11 molecules ACKQSRTUWVX

#1: Protein Helicase SWR1


Mass: 178058.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Fusion protein with C-terminal 3xFLAG / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: DNA helicase
#3: Protein Actin-like protein ARP6


Mass: 50100.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: UniProt: Q12509
#7: Protein SWR1-complex protein 3


Mass: 72648.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: UniProt: P31376
#8: Protein Histone H2A


Mass: 14013.177 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HTA1, GI527_G0001155 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A6A5Q1K4
#9: Protein Histone H2B


Mass: 14280.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HTB1, GI527_G0001154 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A6A5PZQ7
#10: Protein Histone H3


Mass: 15421.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, ...Gene: His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, His3:CG33824, CG33824, His3:CG33827, CG33827, His3:CG33830, CG33830, His3:CG33833, CG33833, His3:CG33836, CG33836, His3:CG33839, CG33839, His3:CG33842, CG33842, His3:CG33845, CG33845, His3:CG33848, CG33848, His3:CG33851, CG33851, His3:CG33854, CG33854, His3:CG33857, CG33857, His3:CG33860, CG33860, His3:CG33863, CG33863, His3:CG33866, CG33866
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02299
#11: Protein Histone H4


Mass: 11408.452 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His4r, BcDNA:RH52884, CG3379, Dmel\CG3379, FBtr0082962, H4r, His4-88CD, His4R, CG3379, Dmel_CG3379
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0B4KFZ9

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Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules BD

#2: Protein Vacuolar protein sorting-associated protein 72 / SWR complex protein 2


Mass: 90709.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: UniProt: Q03388
#4: Protein Vacuolar protein sorting-associated protein 71 / SWR complex protein 6


Mass: 32073.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: UniProt: Q03433

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RuvB-like protein ... , 2 types, 6 molecules EGIFHJ

#5: Protein RuvB-like protein 1


Mass: 91413.242 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: Fusion protein with C-terminal maltose-binding protein
Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: DNA helicase
#6: Protein RuvB-like protein 2 / RUVBL2 / TIP49-homology protein 2 / TIP49b homolog


Mass: 51673.488 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: UniProt: Q12464, DNA helicase

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DNA chain , 2 types, 2 molecules YZ

#12: DNA chain DNA (214-MER)


Mass: 65672.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#13: DNA chain DNA (214-MER)


Mass: 66478.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 20 molecules

#14: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#15: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Native SWR1 bound to nucleosome.COMPLEXEndogenously purified yeast SWR1 complex bound to 60-N-7 nucleosome fragment in the presence of ADP-BeF3.#1-#130NATURAL
2Native SWR1 complexCOMPLEXEndogenously purified yeast SWR1 complex#1-#61NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.43 MDaNO
211.19 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Saccharomyces cerevisiae (brewer's yeast)4932W303
32Saccharomyces cerevisiae (brewer's yeast)4932W303
Buffer solutionpH: 7.6
Details: 80 nM SWR1, 160 nM nucleosomes, 1 mM ADP, 10 mM NaF, 8 mM BeCl2, 0.05% glutaraldehyde, 20 mM HEPES-KOH pH 7.6, 1.5 mM MgCl2, 0.25 mM TCEP, 0.01% IGEPAL CA-630, 1% glycerol
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
20.2 mMEDTA1
32 mMmagnesium chlorideMgCl21
4100 mMsodium chlorideNaCl1
50.01 %IGEPAL CA-6301
61 %glycerol1
70.25 mMTCEP1
81 mMADP1
910 mMsodium flourideNaF1
108 mMberyllium chlorideBeCl21
110.05 %glutaraldehyde1
SpecimenConc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3 second blot time and blot force of 10.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 48543 X / Nominal defocus max: 3600 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7260
Details: Each micrograph was fractionated into 64 frames within a 4 second exposure.

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 525782
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16524 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 200 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16GEJ

6gej

16GEJ1PDBexperimental model
21AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 187.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003151416
ELECTRON MICROSCOPYf_angle_d0.672570830
ELECTRON MICROSCOPYf_chiral_restr0.04797976
ELECTRON MICROSCOPYf_plane_restr0.00667788
ELECTRON MICROSCOPYf_dihedral_angle_d23.34719827

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