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- EMDB-23631: cryo-EM density map of chromatin fiber containing canonical histo... -

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Basic information

Entry
Database: EMDB / ID: EMD-23631
Titlecryo-EM density map of chromatin fiber containing canonical histones and 167-bp 601 DNA
Map datachromatin fiber containing canonical histones and 167-bp 601 DNA sequence
Sample
  • Complex: In-vitro reconstituted chromatin fiber containing canonical histones and twelve tandem repeats of 167-bp 601 Windom sequence
    • Complex: Histones H2A
      • Protein or peptide: Histone H2A
    • Complex: 12x167bp 601 DNA
      • DNA: 12x 167bp 601 DNA
    • Complex: Histone H2B
      • Protein or peptide: Histone H2B
    • Complex: Histone H3
      • Protein or peptide: Histone H3
    • Complex: Histone H4
      • Protein or peptide: Histone H4
Function / homology
Function and homology information


Inhibition of DNA recombination at telomere / DNA Damage/Telomere Stress Induced Senescence / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / Cleavage of the damaged purine / heterochromatin formation => GO:0031507 / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / multicellular organism development ...Inhibition of DNA recombination at telomere / DNA Damage/Telomere Stress Induced Senescence / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / Cleavage of the damaged purine / heterochromatin formation => GO:0031507 / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / multicellular organism development / nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / cellular response to estradiol stimulus / euchromatin / chromatin DNA binding / structural constituent of chromatin / cellular response to insulin stimulus / nucleosome / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
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 / Histone H4, conserved site ...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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / 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. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H3 / Histone H2B 1.1 / Histone H2A.Z / Histone H4
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsLewis T / Sokolova V / Ng H / Tan D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1942049 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM133611 United States
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Structural basis of chromatin regulation by histone variant H2A.Z.
Authors: Tyler S Lewis / Vladyslava Sokolova / Harry Jung / Honkit Ng / Dongyan Tan /
Abstract: The importance of histone variant H2A.Z in transcription regulation has been well established, yet its mechanism-of-action remains enigmatic. Conflicting evidence exists in support of both an ...The importance of histone variant H2A.Z in transcription regulation has been well established, yet its mechanism-of-action remains enigmatic. Conflicting evidence exists in support of both an activating and a repressive role of H2A.Z in transcription. Here we report cryo-electron microscopy (cryo-EM) structures of nucleosomes and chromatin fibers containing H2A.Z and those containing canonical H2A. The structures show that H2A.Z incorporation results in substantial structural changes in both nucleosome and chromatin fiber. While H2A.Z increases the mobility of DNA terminus in nucleosomes, it simultaneously enables nucleosome arrays to form a more regular and condensed chromatin fiber. We also demonstrated that H2A.Z's ability to enhance nucleosomal DNA mobility is largely attributed to its characteristic shorter C-terminus. Our study provides the structural basis for H2A.Z-mediated chromatin regulation, showing that the increase flexibility of the DNA termini in H2A.Z nucleosomes is central to its dual-functions in chromatin regulation and in transcription.
History
DepositionMar 16, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23631.png

Downloads & links

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Map

FileDownload / File: emd_23631.map.gz / Format: CCP4 / Size: 193.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationchromatin fiber containing canonical histones and 167-bp 601 DNA sequence
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.0085 / Movie #1: 0.0085
Minimum - Maximum-0.015277512 - 0.06680051
Average (Standard dev.)2.4462492e-05 (±0.0043158666)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions370370370
Spacing370370370
CellA=B=C: 518.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z370370370
origin x/y/z0.0000.0000.000
length x/y/z518.000518.000518.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ376376376
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS370370370
D min/max/mean-0.0150.0670.000

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Supplemental data

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Sample components

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Entire : In-vitro reconstituted chromatin fiber containing canonical histo...

EntireName: In-vitro reconstituted chromatin fiber containing canonical histones and twelve tandem repeats of 167-bp 601 Windom sequence
Components
  • Complex: In-vitro reconstituted chromatin fiber containing canonical histones and twelve tandem repeats of 167-bp 601 Windom sequence
    • Complex: Histones H2A
      • Protein or peptide: Histone H2A
    • Complex: 12x167bp 601 DNA
      • DNA: 12x 167bp 601 DNA
    • Complex: Histone H2B
      • Protein or peptide: Histone H2B
    • Complex: Histone H3
      • Protein or peptide: Histone H3
    • Complex: Histone H4
      • Protein or peptide: Histone H4

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Supramolecule #1: In-vitro reconstituted chromatin fiber containing canonical histo...

SupramoleculeName: In-vitro reconstituted chromatin fiber containing canonical histones and twelve tandem repeats of 167-bp 601 Windom sequence
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The map was reconstructed through multi-body refinement of the eight nucleosomes at the the center of the fiber
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Supramolecule #2: Histones H2A

SupramoleculeName: Histones H2A / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Supramolecule #3: 12x167bp 601 DNA

SupramoleculeName: 12x167bp 601 DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: unidentified (others)
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)

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Supramolecule #4: Histone H2B

SupramoleculeName: Histone H2B / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Supramolecule #5: Histone H3

SupramoleculeName: Histone H3 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Supramolecule #6: Histone H4

SupramoleculeName: Histone H4 / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

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Macromolecule #2: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPDPAKSAPA AKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVND VFERIAGEAS RLAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV T KYTSAK

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Macromolecule #3: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQ RLVREIAQDF KTDLRFQSSA VMALQEASEA YLVGLFEDTN LCGIHAKRVT I MPKDIQLA RRIRGERA

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRD AVTYTEHAKR KTVTAMDVVY ALKRQGRTLY GFGG

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Macromolecule #5: 12x 167bp 601 DNA

MacromoleculeName: 12x 167bp 601 DNA / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: unidentified (others)
SequenceString: ATCCCGCCCT GGAGAATCCC GGTGCCGAGG CCGCTCAATT GGTCGTAGAC AGCTCTAGCA CCGCTTAAAC GCACGTACGC GCTGTCCCCC GCGTTTTAAC CGCCAAGGGG ATTACTCCCT AGTCTCCAGG CACGTGTCAG ATATATACAT CCTGTGCATG ACTAGATATC ...String:
ATCCCGCCCT GGAGAATCCC GGTGCCGAGG CCGCTCAATT GGTCGTAGAC AGCTCTAGCA CCGCTTAAAC GCACGTACGC GCTGTCCCCC GCGTTTTAAC CGCCAAGGGG ATTACTCCCT AGTCTCCAGG CACGTGTCAG ATATATACAT CCTGTGCATG ACTAGATATC CCGCCCTGGA GAATCCCGGT GCCGAGGCCG CTCAATTGGT CGTAGACAGC TCTAGCACCG CTTAAACGCA CGTACGCGCT GTCCCCCGCG TTTTAACCGC CAAGGGGATT ACTCCCTAGT CTCCAGGCAC GTGTCAGATA TATACATCCT GTGCATGACT AGATATCCCG CCCTGGAGAA TCCCGGTGCC GAGGCCGCTC AATTGGTCGT AGACAGCTCT AGCACCGCTT AAACGCACGT ACGCGCTGTC CCCCGCGTTT TAACCGCCAA GGGGATTACT CCCTAGTCTC CAGGCACGTG TCAGATATAT ACATCCTGTG CATGACTAGA TATCCCGCCC TGGAGAATCC CGGTGCCGAG GCCGCTCAAT TGGTCGTAGA CAGCTCTAGC ACCGCTTAAA CGCACGTACG CGCTGTCCCC CGCGTTTTAA CCGCCAAGGG GATTACTCCC TAGTCTCCAG GCACGTGTCA GATATATACA TCCTGTGCAT GACTAGATAT CCCGCCCTGG AGAATCCCGG TGCCGAGGCC GCTCAATTGG TCGTAGACAG CTCTAGCACC GCTTAAACGC ACGTACGCGC TGTCCCCCGC GTTTTAACCG CCAAGGGGAT TACTCCCTAG TCTCCAGGCA CGTGTCAGAT ATATACATCC TGTGCATGAC TAGATATCCC GCCCTGGAGA ATCCCGGTGC CGAGGCCGCT CAATTGGTCG TAGACAGCTC TAGCACCGCT TAAACGCACG TACGCGCTGT CCCCCGCGTT TTAACCGCCA AGGGGATTAC TCCCTAGTCT CCAGGCACGT GTCAGATATA TACATCCTGT GCATGACTAG ATATCCCGCC CTGGAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTCC CTAGTCTCCA GGCACGTGTC AGATATATAC ATCCTGTGCA TGACTAGATA TCCCGCCCTG GAGAATCCCG GTGCCGAGGC CGCTCAATTG GTCGTAGACA GCTCTAGCAC CGCTTAAACG CACGTACGCG CTGTCCCCCG CGTTTTAACC GCCAAGGGGA TTACTCCCTA GTCTCCAGGC ACGTGTCAGA TATATACATC CTGTGCATGA CTAGATATCC CGCCCTGGAG AATCCCGGTG CCGAGGCCGC TCAATTGGTC GTAGACAGCT CTAGCACCGC TTAAACGCAC GTACGCGCTG TCCCCCGCGT TTTAACCGCC AAGGGGATTA CTCCCTAGTC TCCAGGCACG TGTCAGATAT ATACATCCTG TGCATGACTA GATATCCCGC CCTGGAGAAT CCCGGTGCCG AGGCCGCTCA ATTGGTCGTA GACAGCTCTA GCACCGCTTA AACGCACGTA CGCGCTGTCC CCCGCGTTTT AACCGCCAAG GGGATTACTC CCTAGTCTCC AGGCACGTGT CAGATATATA CATCCTGTGC ATGACTAGAT ATCCCGCCCT GGAGAATCCC GGTGCCGAGG CCGCTCAATT GGTCGTAGAC AGCTCTAGCA CCGCTTAAAC GCACGTACGC GCTGTCCCCC GCGTTTTAAC CGCCAAGGGG ATTACTCCCT AGTCTCCAGG CACGTGTCAG ATATATACAT CCTGTGCATG ACTAGATATC CCGCCCTGGA GAATCCCGGT GCCGAGGCCG CTCAATTGGT CGTAGACAGC TCTAGCACCG CTTAAACGCA CGTACGCGCT GTCCCCCGCG TTTTAACCGC CAAGGGGATT ACTCCCTAGT CTCCAGGCAC GTGTCAGATA TATACATCCT GTGCATGACT AGAT

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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: 8
Component:
ConcentrationFormulaName
2.5 mMNaClSodium chloridesodium chloride
10.0 mMTris
5.0 mMBME2-mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy #1

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Microscopy ID1
Image recordingImage recording ID: 1 / Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 5205 / Average electron dose: 31.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 73000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Microscopy ID1
Image recordingImage recording ID: 2 / Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Number real images: 1950 / Average exposure time: 60.0 sec. / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 192683
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14)
Startup modelType of model: OTHER
Details: Ab-initioin reconstruction in cryoSPARC was performed to generate the initial model.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final 3D classificationNumber classes: 7 / Software - Name: RELION (ver. 3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0)
Details: Multi-body refinement was performed based on the consensus refined map to obtain the final map.
Number images used: 57357
DetailsThe datasets from Krios+K3 were scaled and combined with datasets from Arctica+Falcon3, before thorough image processing.
Image recording ID1
FSC plot (resolution estimation)

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