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- EMDB-44148: The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-44148
TitleThe cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome
Map data
Sample
  • Complex: nucleosome containing histone variants H3.3 and H2A.Z
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.Z
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (128-MER)
    • DNA: DNA (128-MER)
Keywordshistone variant / nucleosome / chromatin / complex / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / nucleus organization / spermatid development / heterochromatin organization ...negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / nucleus organization / spermatid development / heterochromatin organization / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / nucleosomal DNA binding / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / Inhibition of DNA recombination at telomere / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / PRC2 methylates histones and DNA / Defective pyroptosis / cellular response to estradiol stimulus / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / multicellular organism growth / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / osteoblast differentiation / Transcriptional regulation of granulopoiesis / cellular response to insulin stimulus / structural constituent of chromatin / male gonad development / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell population proliferation / chromosome, telomeric region / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / 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 H2B 1.1 / Histone H2A.Z / Histone H4 / Histone H3.3
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Homo sapiens (human) / Xenopus laevis (African clawed frog) / Mus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsTan D / Sokolova V
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133611 United States
National Science Foundation (NSF, United States)1942049 United States
CitationJournal: Epigenomes / Year: 2024
Title: Structural and Biochemical Characterization of the Nucleosome Containing Variants H3.3 and H2A.Z
Authors: Jung H / Sokolova V / Lee G / Stevens VR / Tan D
History
DepositionMar 19, 2024-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44148.png

Downloads & links

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Map

FileDownload / File: emd_44148.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.10620304 - 0.22206807
Average (Standard dev.)0.00021574917 (±0.004335793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44148_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44148_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : nucleosome containing histone variants H3.3 and H2A.Z

EntireName: nucleosome containing histone variants H3.3 and H2A.Z
Components
  • Complex: nucleosome containing histone variants H3.3 and H2A.Z
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.Z
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (128-MER)
    • DNA: DNA (128-MER)

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Supramolecule #1: nucleosome containing histone variants H3.3 and H2A.Z

SupramoleculeName: nucleosome containing histone variants H3.3 and H2A.Z / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The complex contains Xenopus histone H2B and H4, human H3.3, and mouse H2A.Z
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 288 KDa

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Macromolecule #1: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.360983 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAA IGALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.3

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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.Z

MacromoleculeName: Histone H2A.Z / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.581796 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGGKAGKDS GKAKTKAVSR SQRAGLQFPV GRIHRHLKSR TTSHGRVGAT AAVYSAAILE YLTAEVLELA GNASKDLKVK RITPRHLQL AIRGDEELDS LIKATIAGGG VIPHIHKSLI GKKGQQKTV

UniProtKB: Histone H2A.Z

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.965265 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #5: DNA (128-MER)

MacromoleculeName: DNA (128-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.604047 KDa
SequenceString: (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) ...String:
(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 #6: DNA (128-MER)

MacromoleculeName: DNA (128-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.269656 KDa
SequenceString: (DA)(DT)(DC)(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) ...String:
(DA)(DT)(DC)(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)(DT)(DG)(DC)(DA)(DT)(DG) (DA)(DC) (DT)(DA)(DG)(DA)(DT)

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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

Concentration0.8 mg/mL
BufferpH: 7.5 / Details: 20mM Tris-HCl, 5mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.0002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: Freezing condition: blot force 0, blot time 4.5 second.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 5140 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.25 µm / Nominal defocus min: 1.0 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

Particle selectionNumber selected: 1291847
Startup modelType of model: INSILICO MODEL
In silico model: relion-4.0 was used to generate a de novo 3D initial model from selected 2D particles.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 205792
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 320000 / Software - Name: RELION (ver. 4.0)

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Atomic model buiding 1

Initial model
PDB IDChain

5b33

chain_id: A, source_name: PDB, initial_model_type: experimental model

5b33

chain_id: B, source_name: PDB, initial_model_type: experimental model

5b33

chain_id: C, source_name: PDB, initial_model_type: experimental model

5b33

chain_id: D, source_name: PDB, initial_model_type: experimental model

5b33

chain_id: E, source_name: PDB, initial_model_type: experimental model

5b33

chain_id: F, source_name: PDB, initial_model_type: experimental model

5b33

chain_id: G, source_name: PDB, initial_model_type: experimental model

5b33

chain_id: H, source_name: PDB, initial_model_type: experimental model

6fq5

chain_id: I, source_name: PDB, initial_model_type: experimental model

6fq5

chain_id: J, source_name: PDB, initial_model_type: experimental model
DetailsPhenix real-space refinement was used.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 87.42
Output model

PDB-9b3p:
The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome

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