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- EMDB-31106: Snf5 Finger Helix bound to the nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-31106
TitleSnf5 Finger Helix bound to the nucleosome
Map dataThe structure of Snf5 Finger Helix bound to the nucleosome
Sample
  • Complex: Chromatin remodeler complex SWI/SNF, Snf5 Finger Helix bound to the nucleosome
    • Complex: Snf5 Finger Helix
      • Protein or peptide: SWI/SNF chromatin-remodeling complex subunit SNF5
    • Complex: Histone
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA
      • DNA: DNA (235-MER)
      • DNA: DNA (235-MER)
KeywordsChromatin remodeler complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


carbon catabolite activation of transcription / positive regulation of invasive growth in response to glucose limitation / SWI/SNF complex / nuclear chromosome / double-strand break repair via homologous recombination / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / RNA polymerase II-specific DNA-binding transcription factor binding ...carbon catabolite activation of transcription / positive regulation of invasive growth in response to glucose limitation / SWI/SNF complex / nuclear chromosome / double-strand break repair via homologous recombination / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin remodeling / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A ...SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / SWI/SNF chromatin-remodeling complex subunit SNF5 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChen ZC / Chen KJ
CitationJournal: Cell Discov / Year: 2021
Title: Structure of the SWI/SNF complex bound to the nucleosome and insights into the functional modularity.
Authors: Zhenyu He / Kangjing Chen / Youpi Ye / Zhucheng Chen /
History
DepositionMar 24, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0077
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0077
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7eg6
  • Surface level: 0.0077
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31106.png

Downloads & links

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Map

FileDownload / File: emd_31106.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe structure of Snf5 Finger Helix bound to the nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 429.68 Å		1.07 Å/pix.
x 400 pix.
= 429.68 Å		1.07 Å/pix.
x 400 pix.
= 429.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0077 / Movie #1: 0.0077
Minimum - Maximum-0.019681903 - 0.060129233
Average (Standard dev.)0.000042960335 (±0.00092291186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 429.68002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.07421.07421.0742
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z429.680429.680429.680
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0200.0600.000

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Supplemental data

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Sample components

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Entire : Chromatin remodeler complex SWI/SNF, Snf5 Finger Helix bound to t...

EntireName: Chromatin remodeler complex SWI/SNF, Snf5 Finger Helix bound to the nucleosome
Components
  • Complex: Chromatin remodeler complex SWI/SNF, Snf5 Finger Helix bound to the nucleosome
    • Complex: Snf5 Finger Helix
      • Protein or peptide: SWI/SNF chromatin-remodeling complex subunit SNF5
    • Complex: Histone
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA
      • DNA: DNA (235-MER)
      • DNA: DNA (235-MER)

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Supramolecule #1: Chromatin remodeler complex SWI/SNF, Snf5 Finger Helix bound to t...

SupramoleculeName: Chromatin remodeler complex SWI/SNF, Snf5 Finger Helix bound to the nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Snf5 Finger Helix

SupramoleculeName: Snf5 Finger Helix / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Supramolecule #3: Histone

SupramoleculeName: Histone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7

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Macromolecule #1: SWI/SNF chromatin-remodeling complex subunit SNF5

MacromoleculeName: SWI/SNF chromatin-remodeling complex subunit SNF5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 102.642172 KDa
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
SequenceString: MNNQPQGTNS VPNSIGNIFS NIGTPSFNMA QIPQQLYQSL TPQQLQMIQQ RHQQLLRSRL QQQQQQQQQT SPPPQTHQSP PPPPQQSQP IANQSATSTP PPPPAPHNLH PQIGQVPLAP APINLPPQIA QLPLATQQQV LNKLRQQAIA KNNPQVVNAI T VAQQQVQR ...String:
MNNQPQGTNS VPNSIGNIFS NIGTPSFNMA QIPQQLYQSL TPQQLQMIQQ RHQQLLRSRL QQQQQQQQQT SPPPQTHQSP PPPPQQSQP IANQSATSTP PPPPAPHNLH PQIGQVPLAP APINLPPQIA QLPLATQQQV LNKLRQQAIA KNNPQVVNAI T VAQQQVQR QIEQQKGQQT AQTQLEQQRQ LLVQQQQQQQ LRNQIQRQQQ QQFRHHVQIQ QQQQKQQQQQ QQHQQQQQQQ QQ QQQQQQQ QQQQQQQQQQ QQQQQQQQQQ QGQIPQSQQV PQVRSMSGQP PTNVQPTIGQ LPQLPKLNLP KYQTIQYDPP ETK LPYPTY WSDKKADTDT LLYEQIIQRD KINKYSLIRE TNGYDPFSIY GFSNKEYISR LWHTLKYYQD LKNTRMKSIT STSQ KIPSA SIWGNGYSGY GNGITNTTTR VIPQVEVGNR KHYLEDKLKV YKQAMNETSE QLVPIRLEFD QDRDRFFLRD TLLWN KNDK LIKIEDFVDD MLRDYRFEDA TREQHIDTIC QSIQEQIQEF QGNPYIELNQ DRLGGDDLRI RIKLDIVVGQ NQLIDQ FEW DISNSDNCPE EFAESMCQEL ELPGEFVTAI AHSIREQVHM YHKSLALLGY NFDGSAIEDD DIRSRMLPTI TLDDVYR PA AESKIFTPNL LQISAAELER LDKDKDRDTR RKRRQGRSNR RGMLALSGTS ASNTSMNGVH NTVAAGNASS LPPGEILL P DIADIPRTFR TPVPSTLMPG GVDVGPSVES YELRNTTTYK SRPDRPKPVS PPCYIIDHIP GHSLLLSIKL PGKVNTKEE FAAAPNDTSS GTNAMLPSPE SLKTKLNSNI RAGVTIPSIP NPIANHTVTN SPNPTLQPVI PGGAASKSVP TPSLPIAPPV APHDSEATL LTNSNNGSSN NNTQNT

UniProtKB: SWI/SNF chromatin-remodeling complex subunit SNF5

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Macromolecule #2: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.289904 KDa
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #4: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A type 1

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Macromolecule #5: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B 1.1

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Macromolecule #6: DNA (235-MER)

MacromoleculeName: DNA (235-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 72.380109 KDa
SequenceString: (DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DT)(DG) (DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA)(DC) (DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC) (DC)(DG)(DG)(DT)(DG)(DC) ...String:
(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DT)(DG) (DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA)(DC) (DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (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)(DA)(DA)(DG)(DC)(DT) (DT) (DG)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DG)(DT) (DA)(DC)(DT)(DA)(DG)(DA)(DG)(DG)(DA) (DT)(DC)(DA)(DT)(DA)(DA)(DT)(DC)(DA)(DG) (DC)(DC)(DA)(DT)(DA)(DC)(DC)(DA)(DC)(DA) (DT)(DT)(DT)(DG)(DT)(DA)(DG)(DA)(DG) (DG)(DT)(DT)(DT)(DT)(DA)

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Macromolecule #7: DNA (235-MER)

MacromoleculeName: DNA (235-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 72.740328 KDa
SequenceString: (DT)(DA)(DA)(DA)(DA)(DC)(DC)(DT)(DC)(DT) (DA)(DC)(DA)(DA)(DA)(DT)(DG)(DT)(DG)(DG) (DT)(DA)(DT)(DG)(DG)(DC)(DT)(DG)(DA) (DT)(DT)(DA)(DT)(DG)(DA)(DT)(DC)(DC)(DT) (DC) (DT)(DA)(DG)(DT)(DA)(DC) ...String:
(DT)(DA)(DA)(DA)(DA)(DC)(DC)(DT)(DC)(DT) (DA)(DC)(DA)(DA)(DA)(DT)(DG)(DT)(DG)(DG) (DT)(DA)(DT)(DG)(DG)(DC)(DT)(DG)(DA) (DT)(DT)(DA)(DT)(DG)(DA)(DT)(DC)(DC)(DT) (DC) (DT)(DA)(DG)(DT)(DA)(DC)(DT)(DT) (DC)(DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC) (DT)(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)(DC)(DA)(DG)(DG)(DG)(DC)(DG) (DG)(DC)(DC)(DG)(DC)(DG)(DT)(DA)(DT)(DA) (DG)(DG)(DG)(DT)(DC)(DC)(DA)(DT)(DC) (DA)(DC)(DA)(DT)(DA)(DA)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 525389
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER

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