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- EMDB-47428: SNF2H bound to nucleosome - Class E2 -

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Basic information

Entry
Database: EMDB / ID: EMD-47428
TitleSNF2H bound to nucleosome - Class E2
Map dataSNF2H bound to nucleosome - Class E2
Sample
  • Complex: SNF2H bound to nucleosome - Class E2
  • Protein or peptide: Histone H2A
  • Protein or peptide: Histone H2B 1.1
  • Protein or peptide: Histone H3
  • Protein or peptide: Histone H4
  • Protein or peptide: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5
  • DNA: Chain I (DNA)
  • DNA: Chain J (DNA)
KeywordsChromatin / remodeler / DNA BINDING PROTEIN
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
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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMalik D / Deshmukh AA / Bilokapic S / Halic M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM135599-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141694-01 United States
CitationJournal: bioRxiv / Year: 2025
Title: Mechanisms of chromatin remodeling by an Snf2-type ATPase.
Authors: Deepshikha Malik / Ashish Deshmukh / Silvija Bilokapic / Mario Halic /
Abstract: Chromatin remodeling enzymes play a crucial role in the organization of chromatin, enabling both stability and plasticity of genome regulation. These enzymes use a Snf2-type ATPase motor to move ...Chromatin remodeling enzymes play a crucial role in the organization of chromatin, enabling both stability and plasticity of genome regulation. These enzymes use a Snf2-type ATPase motor to move nucleosomes, but how they translocate DNA around the histone octamer is unclear. Here we use cryo-EM to visualize the continuous motion of nucleosomal DNA induced by human chromatin remodeler SNF2H, an ISWI family member. Our work reveals conformational changes in SNF2H, DNA and histones during nucleosome sliding and provides the structural basis for DNA translocation. ATP hydrolysis induces conformational changes in SNF2H that pull the DNA tracking strand, distorting DNA and histones at SHL2. This is followed by SNF2H rotation on the nucleosome, which first pulls the DNA guide strand and creates one-base pair bulge at SHL2, and then releases the pulled DNA. Given the high conservation of the catalytic motors among ATP-dependent chromatin remodelers, the mechanisms we describe likely apply to other families.
History
DepositionOct 21, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47428.png

Downloads & links

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Map

FileDownload / File: emd_47428.map.gz / Format: CCP4 / Size: 468.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSNF2H bound to nucleosome - Class E2
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 497 pix.
= 497. Å		1 Å/pix.
x 497 pix.
= 497. Å		1 Å/pix.
x 497 pix.
= 497. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.239
Minimum - Maximum-0.4659074 - 33.769992999999999
Average (Standard dev.)-0.023204057 (±0.26807055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions497497497
Spacing497497497
CellA=B=C: 497.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_47428_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_47428_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SNF2H bound to nucleosome - Class E2

EntireName: SNF2H bound to nucleosome - Class E2
Components
  • Complex: SNF2H bound to nucleosome - Class E2
  • Protein or peptide: Histone H2A
  • Protein or peptide: Histone H2B 1.1
  • Protein or peptide: Histone H3
  • Protein or peptide: Histone H4
  • Protein or peptide: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5
  • DNA: Chain I (DNA)
  • DNA: Chain J (DNA)

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Supramolecule #1: SNF2H bound to nucleosome - Class E2

SupramoleculeName: SNF2H bound to nucleosome - Class E2 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A type 1

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Macromolecule #2: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKTRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #3: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #5: 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: 5 / Enantiomer: LEVO
SequenceString: MSSAAEPPPP PPPESAPSKP AASIASGGSN SSNKGGPEGV AAQAVASAAS AGPADAEMEE IFDDASPGKQ KEIQEPDPTY EEKMQTDRAN RFEYLLKQTE LFAHFIQPAA QKTPTSPLKM KPGRPRIKKD EKQNLLSVGD YRHRRTEQEE DEELLTESSK ATNVCTRFED ...String:
MSSAAEPPPP PPPESAPSKP AASIASGGSN SSNKGGPEGV AAQAVASAAS AGPADAEMEE IFDDASPGKQ KEIQEPDPTY EEKMQTDRAN RFEYLLKQTE LFAHFIQPAA QKTPTSPLKM KPGRPRIKKD EKQNLLSVGD YRHRRTEQEE DEELLTESSK ATNVCTRFED SPSYVKWGKL RDYQVRGLNW LISLYENGIN GILADEMGLG KTLQTISLLG YMKHYRNIPG PHMVLVPKST LHNWMSEFKR WVPTLRSVCL IGDKEQRAAF VRDVLLPGEW DVCVTSYEML IKEKSVFKKF NWRYLVIDEA HRIKNEKSKL SEIVREFKTT NRLLLTGTPL QNNLHELWSL LNFLLPDVFN SADDFDSWFD TNNCLGDQKL VERLHMVLRP FLLRRIKADV EKSLPPKKEV KIYVGLSKMQ REWYTRILMK DIDILNSAGK MDKMRLLNIL MQLRKCCNHP YLFDGAEPGP PYTTDMHLVT NSGKMVVLDK LLPKLKEQGS RVLIFSQMTR VLDILEDYCM WRNYEYCRLD GQTPHDERQD SINAYNEPNS TKFVFMLSTR AGGLGINLAT ADVVILYDSD WNPQVDLQAM DRAHRIGQTK TVRVFRFITD NTVEERIVER AEMKLRLDSI VIQQGRLVDQ NLNKIGKDEM LQMIRHGATH VFASKESEIT DEDIDGILER GAKKTAEMNE KLSKMGESSL RNFTMDTESS VYNFEGEDYR EKQKIAFTEW IEPPKRERKA NYAVDAYFRE ALRVSEPKAP KAPRPPKQPN VQDFQFFPPR LFELLEKEIL FYRKTIGYKV PRNPELPNAA QAQKEEQLKI DEAESLNDEE LEEKEKLLTQ GFTNWNKRDF NQFIKANEKW GRDDIENIAR EVEGKTPEEV IEYSAVFWER CNELQDIEKI MAQIERGEAR IQRRISIKKA LDTKIGRYKA PFHQLRISYG TNKGKNYTEE EDRFLICMLH KLGFDKENVY DELRQCIRNS PQFRFDWFLK SRTAMELQRR CNTLITLIER ENMELEEKEK AEKKKRGPKP STQKRKMDGA PDGRGRKKKL KL

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

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Macromolecule #6: Chain I (DNA)

MacromoleculeName: Chain I (DNA) / type: dna / ID: 6 / Classification: DNA
SequenceString:
ACAGGATGTA TATATCTGAC ACGTGCCTGG AGACTAGGGA GTAATCCCCT TGGCGGtTAA AACGCGGGGG ACAGCGCGTA CGTGCGTTTA AGCGGTGCTA GAGCTGTCTA CGACCAATTG AGCGGCCTCG GCACCGGGAT TCTCCAGGG

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Macromolecule #7: Chain J (DNA)

MacromoleculeName: Chain J (DNA) / type: dna / ID: 7 / Classification: DNA
SequenceString:
CCCTGGAGAA TCCCGGTGCC GAGGCCGCTC AATTGGTCGT AGACAGCTCT AGCACCGCTT AAACGCACGT ACGCGCTGTC CCCCGCGTTT TAaCCGCCAA GGGGATTACT CCCTAGTCTC CAGGCACGTG TCAGATATAT ACATCCTGTG CA

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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 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber temperature: 285.65 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 160.0 K / Max: 175.0 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

21970

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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