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- EMDB-21484: Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosom... -

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Basic information

Entry
Database: EMDB / ID: EMD-21484
TitleCryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state
Map datacryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; unsharpened map
Sample
  • Complex: cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state
    • Complex: Histone H3, Histone H4, Histone H2A, Histone H2B
      • Protein or peptide: x 4 types
    • Complex: DNA
      • DNA: x 2 types
    • Complex: Nuclear protein STH1/NPS1, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102
      • Protein or peptide: x 4 types
  • Ligand: x 4 types
KeywordsChromatin remodeling / Nucleosome / Gene Regulation / MOTOR PROTEIN
Function / homology
Function and homology information


RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / Platelet degranulation / DNA translocase activity / RSC-type complex / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity ...RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / Platelet degranulation / DNA translocase activity / RSC-type complex / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / NuA4 histone acetyltransferase complex / chromosome, centromeric region / ATP-dependent activity, acting on DNA / cytoskeleton organization / histone reader activity / meiotic cell cycle / chromosome segregation / helicase activity / transcription elongation by RNA polymerase II / lysine-acetylated histone binding / base-excision repair / structural constituent of chromatin / nucleosome / double-strand break repair / nucleosome assembly / chromatin organization / DNA helicase / chromatin remodeling / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / structural molecule activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus
Similarity search - Function
Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily ...Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Helicase conserved C-terminal domain / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Nuclear protein STH1/NPS1 / Regulator of Ty1 transposition protein 102 / Histone H4 / Actin-like protein ARP9 / Actin-related protein 7 / Histone H2A / Histone H2B / Histone H3
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / synthetic construct (others) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLeschziner AE / Baker RW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM092895-08 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structural insights into assembly and function of the RSC chromatin remodeling complex.
Authors: Richard W Baker / Janice M Reimer / Peter J Carman / Bengi Turegun / Tsutomu Arakawa / Roberto Dominguez / Andres E Leschziner /
Abstract: SWI/SNF chromatin remodelers modify the position and spacing of nucleosomes and, in humans, are linked to cancer. To provide insights into the assembly and regulation of this protein family, we ...SWI/SNF chromatin remodelers modify the position and spacing of nucleosomes and, in humans, are linked to cancer. To provide insights into the assembly and regulation of this protein family, we focused on a subcomplex of the Saccharomyces cerevisiae RSC comprising its ATPase (Sth1), the essential actin-related proteins (ARPs) Arp7 and Arp9 and the ARP-binding protein Rtt102. Cryo-EM and biochemical analyses of this subcomplex shows that ARP binding induces a helical conformation in the helicase-SANT-associated (HSA) domain of Sth1. Surprisingly, the ARP module is rotated 120° relative to the full RSC about a pivot point previously identified as a regulatory hub in Sth1, suggesting that large conformational changes are part of Sth1 regulation and RSC assembly. We also show that a conserved interaction between Sth1 and the nucleosome acidic patch enhances remodeling. As some cancer-associated mutations dysregulate rather than inactivate SWI/SNF remodelers, our insights into RSC complex regulation advance a mechanistic understanding of chromatin remodeling in disease states.
History
DepositionFeb 27, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vz4
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vz4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21484.png

Downloads & links

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Map

FileDownload / File: emd_21484.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; unsharpened map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 300 pix.
= 348. Å		1.16 Å/pix.
x 300 pix.
= 348. Å		1.16 Å/pix.
x 300 pix.
= 348. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

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Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.013
Minimum - Maximum-0.014125751 - 0.055047
Average (Standard dev.)0.00015059518 (±0.0023496093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z348.000348.000348.000
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0140.0550.000

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Supplemental data

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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_1.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; sharpened map
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_10.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 3; unsharpened map
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_11.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 3; half map 1
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_12.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 3; sharpened map
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_13.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 3; half map 2
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_2.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 1; half map 2
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_3.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 1; unsharpened map
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_4.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 1; half map 2
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_5.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 1; sharpened map
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_6.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 2; unsharpened map
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_7.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 2; half map 1
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_8.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 2; half map 2
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Additional map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_additional_9.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; Multi Body Refinement Body 2; sharpened map
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Half map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_half_map_1.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; half map 1
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Half map: cryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome;...

Fileemd_21484_half_map_2.map
Annotationcryo-EM map of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome; half map 2
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Sample components

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Entire : cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosom...

EntireName: cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state
Components
  • Complex: cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state
    • Complex: Histone H3, Histone H4, Histone H2A, Histone H2B
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: DNA
      • DNA: DNA (185-MER)
      • DNA: DNA (185-MER)
    • Complex: Nuclear protein STH1/NPS1, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102
      • Protein or peptide: Nuclear protein STH1/NPS1
      • Protein or peptide: Actin-related protein 7
      • Protein or peptide: Actin-like protein ARP9
      • Protein or peptide: Regulator of Ty1 transposition protein 102
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosom...

SupramoleculeName: cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Molecular weightTheoretical: 440 KDa

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Supramolecule #2: Histone H3, Histone H4, Histone H2A, Histone H2B

SupramoleculeName: Histone H3, Histone H4, Histone H2A, Histone H2B / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: Nuclear protein STH1/NPS1, Actin-related protein 7, Actin-like pr...

SupramoleculeName: Nuclear protein STH1/NPS1, Actin-related protein 7, Actin-like protein ARP9, Regulator of Ty1 transposition protein 102
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#10
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.407075 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LCGIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.810048 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MPDPAKSAPA AKKGSKKAVT KTQKKDGKKR RKTRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSA

UniProtKB: Histone H2B

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Macromolecule #7: Nuclear protein STH1/NPS1

MacromoleculeName: Nuclear protein STH1/NPS1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 95.105297 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSHHHHHH SQDPNSVRLA EELERQQLLE KRKKERNLHL QKINSIIDFI KERQSEQWSR QERCFQFGRL GASLHNQMEK DEQKRIERT AKQRLAALKS NDEEAYLKLL DQTKDTRITQ LLRQTNSFLD SLSEAVRAQQ NEAKILHGEE VQPITDEERE K TDYYEVAH ...String:
MGSSHHHHHH SQDPNSVRLA EELERQQLLE KRKKERNLHL QKINSIIDFI KERQSEQWSR QERCFQFGRL GASLHNQMEK DEQKRIERT AKQRLAALKS NDEEAYLKLL DQTKDTRITQ LLRQTNSFLD SLSEAVRAQQ NEAKILHGEE VQPITDEERE K TDYYEVAH RIKEKIDKQP SILVGGTLKE YQLRGLEWMV SLYNNHLNGI LADEMGLGKT IQSISLITYL YEVKKDIGPF LV IVPLSTI TNWTLEFEKW APSLNTIIYK GTPNQRHSLQ HQIRVGNFDV LLTTYEYIIK DKSLLSKHDW AHMIIDEGHR MKN AQSKLS FTISHYYRTR NRLILTGTPL QNNLPELWAL LNFVLPKIFN SAKTFEDWFN TPFANTGTQE KLELTEEETL LIIR RLHKV LRPFLLRRLK KEVEKDLPDK VEKVIKCKLS GLQQQLYQQM LKHNALFVGA GTEGATKGGI KGLNNKIMQL RKICN HPFV FDEVEGVVNP SRGNSDLLFR VAGKFELLDR VLPKFKASGH RVLMFFQMTQ VMDIMEDFLR MKDLKYMRLD GSTKTE ERT EMLNAFNAPD SDYFCFLLST RAGGLGLNLQ TADTVIIFDT DWNPHQDLQA QDRAHRIGQK NEVRILRLIT TDSVEEV IL ERAMQKLDID GKVIQAGKFD NKSTAEEQEA FLRRLIESET NRDDDDKAEL DDDELNDTLA RSADEKILFD KIDKERMN Q ERADAKAQGL RVPPPRLIQL DELPKVFRED IEEHFKKEDS EPLGRIRQKK RVYYDDGLTE EQFLEAVEDD NMSLEDAIK KRREARERRR LRQ

UniProtKB: Nuclear protein STH1/NPS1

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Macromolecule #8: Actin-related protein 7

MacromoleculeName: Actin-related protein 7 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 53.863016 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTLNRKCVVI HNGSHRTVAG FSNVELPQCI IPSSYIKRTD EGGEAEFIFG TYNMIDAAAE KRNGDEVYTL VDSQGLPYNW DALEMQWRY LYDTQLKVSP EELPLVITMP ATNGKPDMAI LERYYELAFD KLNVPVFQIV IEPLAIALSM GKSSAFVIDI G ASGCNVTP ...String:
MTLNRKCVVI HNGSHRTVAG FSNVELPQCI IPSSYIKRTD EGGEAEFIFG TYNMIDAAAE KRNGDEVYTL VDSQGLPYNW DALEMQWRY LYDTQLKVSP EELPLVITMP ATNGKPDMAI LERYYELAFD KLNVPVFQIV IEPLAIALSM GKSSAFVIDI G ASGCNVTP IIDGIVVKNA VVRSKFGGDF LDFQVHERLA PLIKEENDME NMADEQKRST DVWYEASTWI QQFKSTMLQV SE KDLFELE RYYKEQADIY AKQQEQLKQM DQQLQYTALT GSPNNPLVQK KNFLFKPLNK TLTLDLKECY QFAEYLFKPQ LIS DKFSPE DGLGPLMAKS VKKAGASINS MKANTSTNPN GLGTSHINTN VGDNNSTASS SNISPEQVYS LLLTNVIITG STSL IEGME QRIIKELSIR FPQYKLTTFA NQVMMDRKIQ GWLGALTMAN LPSWSLGKWY SKEDYETLKR DRKQSQATNA TN

UniProtKB: Actin-related protein 7

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Macromolecule #9: Actin-like protein ARP9

MacromoleculeName: Actin-like protein ARP9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 53.13193 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAPFRQDSIL IIYPRSQTTL VQFGLNEETF TVPELEIPTQ IYRTTRQDGS YTYHSTNKDN KAELIKPIQN GEIIDISAFT QFLRLIFVS ILSDRANKNQ DAFEAELSNI PLLLITHHSW SQSDLEIITQ YVFESLEINN LIQLPASLAA TYSMISLQNC C IIDVGTHH ...String:
MAPFRQDSIL IIYPRSQTTL VQFGLNEETF TVPELEIPTQ IYRTTRQDGS YTYHSTNKDN KAELIKPIQN GEIIDISAFT QFLRLIFVS ILSDRANKNQ DAFEAELSNI PLLLITHHSW SQSDLEIITQ YVFESLEINN LIQLPASLAA TYSMISLQNC C IIDVGTHH TDIIPIVDYA QLDHLVSSIP MGGQSINDSL KKLLPQWDDD QIESLKKSPI FEVLSDDAKK LSSFDFGNEN ED EDEGTLN VAEIITSGRD TREVLEERER GQKVKNVKNS DLEFNTFWDE KGNEIKVGKQ RFQGCNNLIK NISNRVGLTL DNI DDINKA KAVWENIIIV GGTTSISGFK EALLGQLLKD HLIIEPEEEK SKREEEAKSV LPAATKKKSK FMTNSTAFVP TIEY VQCPT VIKLAKYPDY FPEWKKSGYS EIIFLGAQIV SKQIFTHPKD TFYITREKYN MKGPAALWDV QF

UniProtKB: Actin-like protein ARP9

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Macromolecule #10: Regulator of Ty1 transposition protein 102

MacromoleculeName: Regulator of Ty1 transposition protein 102 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.817615 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MDPQTLITKA NKVSYYGNPT SKESWRYDWY QPSKVSSNVQ QPQQQLGDME NNLEKYPFRY KTWLRNQEDE KNLQRESCED ILDLKEFDR RILKKSLMTS HTKGDTSKAT GAPSANQGDE ALSVDDIRGA VGNSEAIPGL SAGVNNDNTK ESKDVKMN

UniProtKB: Regulator of Ty1 transposition protein 102

+
Macromolecule #5: DNA (185-MER)

MacromoleculeName: DNA (185-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 56.840203 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DC)(DC)(DT)(DA)(DG) (DG)(DT)(DC)(DT)(DC)(DT)(DG)(DA)(DT)(DG) (DC)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA) (DG)(DG)(DC)(DC)(DG)(DC) ...String:
(DA)(DT)(DC)(DA)(DC)(DC)(DC)(DT)(DA)(DG) (DG)(DT)(DC)(DT)(DC)(DT)(DG)(DA)(DT)(DG) (DC)(DT)(DC)(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) (DA)(DC)(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)(DA)(DC)(DA)(DC)(DG)(DC) (DG)(DG)(DT)(DG)(DA)(DA)(DC)(DA) (DG) (DC)(DG)(DA)(DT)

+
Macromolecule #6: DNA (185-MER)

MacromoleculeName: DNA (185-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 57.400555 KDa
SequenceString: (DA)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT)(DC) (DA)(DC)(DC)(DG)(DC)(DG)(DA)(DG)(DT)(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) ...String:
(DA)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT)(DC) (DA)(DC)(DC)(DG)(DC)(DG)(DA)(DG)(DT)(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)(DG) (DT)(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) (DG)(DA)(DG)(DC)(DA)(DT)(DC)(DA)(DG)(DA) (DG)(DA)(DC)(DC)(DT)(DA)(DG)(DG) (DG) (DT)(DG)(DA)(DT)

+
Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

+
Macromolecule #13: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

+
Macromolecule #14: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 14 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: Glow discharge for 30 seconds at 25 mAmp
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 4 second blot time, blot force 20.
DetailsSample was crosslinked using the GRAFIX protocol

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 7.0 sec. / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER / Details: Ab initio model generation in cryoSPARC v2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 293940
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5z3u

source_name: PDB, initial_model_type: experimental model

4i6m

source_name: PDB, initial_model_type: experimental model

5tgc

source_name: PDB, initial_model_type: experimental model
DetailsInitial model docking was done in Chimera. Phenix.real_space_refine was used to refine the nucleosome model. Sth1-Arp7-Arp9-Rtt102 were refined in Rosetta and the top ten models were deposited.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6vz4:
Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state

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