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- EMDB-9356: Cryo-EM structure of singly-bound SNF2h-nucleosome complex with S... -

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Basic information

Entry
Database: EMDB / ID: EMD-9356
TitleCryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at the flanking DNA proximal side
Map datacryosparc v2 non-uniform refinement; sharpened and resampled to fit into common orientation
Sample
  • Complex: Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at the flanking DNA proximal side
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H2B
    • DNA: DNA (156-MER)
    • DNA: DNA (156-MER)
  • Protein or peptide: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsISWI / Chromatin / Nucleosome / DNA / SNF2h / histones / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


RSF complex / histone octamer slider activity / ACF complex / WICH complex / negative regulation of mitotic chromosome condensation / CERF complex / CHRAC / NoRC complex / NURF complex / B-WICH complex ...RSF complex / histone octamer slider activity / ACF complex / WICH complex / negative regulation of mitotic chromosome condensation / CERF complex / CHRAC / NoRC complex / NURF complex / B-WICH complex / nucleosome array spacer activity / rDNA heterochromatin formation / ATP-dependent chromatin remodeler activity / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / positive regulation of transcription by RNA polymerase III / DNA methylation-dependent constitutive heterochromatin formation / positive regulation of transcription by RNA polymerase I / regulation of DNA replication / pericentric heterochromatin / nucleosome binding / condensed chromosome / Deposition of new CENPA-containing nucleosomes at the centromere / antiviral innate immune response / cellular response to leukemia inhibitory factor / positive regulation of DNA replication / helicase activity / DNA-templated transcription initiation / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / fibrillar center / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / site of double-strand break / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA damage response / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleolus / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / SANT domain profile. / SANT domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal ...ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / SANT domain profile. / SANT domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / : / 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 / Helicase conserved C-terminal domain / Histone H3 signature 1. / Homeobox-like domain superfamily / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / 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 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsArmache J-P / Gamarra N / Johnson SL / Leonard JD / Wu S / Narlikar GN
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM073767 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM108455 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM082893 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1S10OD020054 United States
Other governmentUCSF Program for Breakthrough Biomedical Research - New Technology Award United States
CitationJournal: Elife / Year: 2019
Title: Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome.
Authors: Jean Paul Armache / Nathan Gamarra / Stephanie L Johnson / John D Leonard / Shenping Wu / Geeta J Narlikar / Yifan Cheng /
Abstract: The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome ...The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeF that capture two potential reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, appear disordered. The disordered acidic patch is expected to inhibit the second SNF2h protomer, while disorder near the dyad is expected to promote DNA translocation. The other structure doesn't show octamer deformation, but surprisingly shows a 2 bp translocation. FRET studies indicate that ADP-BeF predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation.
History
DepositionDec 16, 2018-
Header (metadata) releaseJul 17, 2019-
Map releaseJul 17, 2019-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ne3
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9356.png

Downloads & links

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Map

FileDownload / File: emd_9356.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryosparc v2 non-uniform refinement; sharpened and resampled to fit into common orientation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 300 pix.
= 364.68 Å		1.22 Å/pix.
x 300 pix.
= 364.68 Å		1.22 Å/pix.
x 300 pix.
= 364.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.245 / Movie #1: 0.3
Minimum - Maximum-1.1748977 - 2.0529401
Average (Standard dev.)0.0008422989 (±0.07229055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 364.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21561.21561.2156
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z364.680364.680364.680
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-1.1752.0530.001

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of singly-bound SNF2h-nucleosome complex with S...

EntireName: Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at the flanking DNA proximal side
Components
  • Complex: Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at the flanking DNA proximal side
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H2B
    • DNA: DNA (156-MER)
    • DNA: DNA (156-MER)
  • Protein or peptide: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Cryo-EM structure of singly-bound SNF2h-nucleosome complex with S...

SupramoleculeName: Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at the flanking DNA proximal side
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 340 kDa/nm

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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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 (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.093436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESAKSAKS K

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.179959 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KKRRKTRKES YAIYVYKVLK QVHPDTGISS KAMSIMNSFV NDVFERIAGE ASRLAHYNKR STITSREIQT AVRLLLPGEL AKHAVSEGT KAVTKYTSAK

UniProtKB: Histone H2B

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Macromolecule #5: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.348852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TRKESYAIYV YKVLKQVHPD TGISSKAMSI MNSFVNDVFE RIAGEASRLA HYNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTK YTSA

UniProtKB: Histone H2B

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Macromolecule #8: SWI/SNF-related matrix-associated actin-dependent regulator of ch...

MacromoleculeName: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.653332 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TRFEDSPSYV KWGKLRDYQV RGLNWLISLY ENGINGILAD EMGLGKTLQT ISLLGYMKHY RNIPGPHMVL VPKSTLHNWM SEFKRWVPT LRSVCLIGDK EQRAAFVRDV LLPGEWDVCV TSYEMLIKEK SVFKKFNWRY LVIDEAHRIK NEKSKLSEIV R EFKTTNRL ...String:
TRFEDSPSYV KWGKLRDYQV RGLNWLISLY ENGINGILAD EMGLGKTLQT ISLLGYMKHY RNIPGPHMVL VPKSTLHNWM SEFKRWVPT LRSVCLIGDK EQRAAFVRDV LLPGEWDVCV TSYEMLIKEK SVFKKFNWRY LVIDEAHRIK NEKSKLSEIV R EFKTTNRL LLTGTPLQNN LHELWSLLNF LLPDVFNSAD DFDSWFDTNC LGQKLVERLH MVLRPFLLRR IKADVEKSLP PK KEVKIYV GLSKMQREWY TRILMKDIDI LNSAGKMDKM RLLNILMQLR KCCNHPYLFD GAEPGPPYTT DMHLVTNSGK MVV LDKLLP KLKEQGSRVL IFSQMTRVLD ILEDYCMWRN YEYCRLDGQT PHDERQDSIN AYNEPNSTKF VFMLSTRAGG LGIN LATAD VVILYDSDWN PQVDLQAMDR AHRIGQTKTV RVFRFITDNT VEERIVERAE MKLRLDSIVI QQ

UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5

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Macromolecule #6: DNA (156-MER)

MacromoleculeName: DNA (156-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 47.936531 KDa
SequenceString: (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) (DA)(DC)(DA)(DG)(DC)(DT) ...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) (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)(DT)(DG)(DC)(DA)(DT)(DG)(DT) (DA)(DT)(DT)

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Macromolecule #7: DNA (156-MER)

MacromoleculeName: DNA (156-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 48.372832 KDa
SequenceString: (DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC)(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) ...String:
(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC)(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)(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) (DC)(DA)(DG)

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, 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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK I
Details: 2.5 ul of nucleosome-443 SNF2h complexes were applied to a glow discharged Quantifoil holey carbon grid (1.2 um hole size, 400 mesh), blotted in a Vitrobot Mark I (FEI Company) using 6 ...Details: 2.5 ul of nucleosome-443 SNF2h complexes were applied to a glow discharged Quantifoil holey carbon grid (1.2 um hole size, 400 mesh), blotted in a Vitrobot Mark I (FEI Company) using 6 seconds blotting at 100% humidity, and then plunge-frozen in liquid ethane cooled by liquid nitrogen..
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsFrames were motion corrected using MotionCor2 with dose-weighting
Particle selectionNumber selected: 95879
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Generated using cryosparc ab initio run
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27513
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6ne3:
Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at SHL-2

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