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- PDB-7m1x: Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z -

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Basic information

Entry
Database: PDB / ID: 7m1x
TitleCryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z
Components
  • (DNA (136-MER)) x 2
  • Histone H2A.Z
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / chromatin / nucleosome / histone variant / epigenetics / transcription / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B 1.1 / Histone H2A.Z / Histone H4
Similarity search - Component
Biological speciesunidentified (others)
Xenopus laevis (African clawed frog)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsTan, D. / Lewis, T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM133611 United States
National Science Foundation (NSF, United States)1942049 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 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
I: DNA (136-MER)
J: DNA (136-MER)
A: Histone H3
B: Histone H4
C: Histone H2A.Z
D: Histone H2B 1.1
E: Histone H3
F: Histone H4
G: Histone H2A.Z
H: Histone H2B 1.1


Theoretical massNumber of molelcules
Total (without water)199,67510
Polymers199,67510
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, This model was refined in Phenix using a initial model generated from PDB:1F66 and PDB:6FQ5.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 2 types, 2 molecules IJ

#1: DNA chain DNA (136-MER)


Mass: 45604.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli DH5[alpha] (bacteria)
#2: DNA chain DNA (136-MER)


Mass: 45145.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli DH5[alpha] (bacteria)

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Protein , 4 types, 8 molecules AEBFCGDH

#3: Protein Histone H3 /


Mass: 15507.190 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Plasmid: pET3C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A310TTQ1
#4: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62799
#5: Protein Histone H2A.Z / / H2A/z


Mass: 13581.796 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2az1, H2afz, H2az / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0C0S6
#6: Protein Histone H2B 1.1 / H2B1.1


Mass: 13979.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02281

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Nucleosome core particle containing variant H2A.Z and canonical core histonesCOMPLEXall0RECOMBINANT
2Histone H3COMPLEX#31RECOMBINANT
3Histone H4COMPLEX#41RECOMBINANT
4Histone variant H2A.ZCOMPLEX#51RECOMBINANT
5Histone H2BCOMPLEX#61RECOMBINANT
6DNA (136-MER)COMPLEX#11RECOMBINANT
7DNA (136-MER)COMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Xenopus laevis (African clawed frog)8355
33Xenopus laevis (African clawed frog)8355
34Mus musculus (house mouse)10090
45Xenopus laevis (African clawed frog)8355
56unidentified (others)32644
67unidentified (others)32644
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Escherichia coli BL21(DE3) (bacteria)469008
43Escherichia coli BL21(DE3) (bacteria)469008
54Escherichia coli BL21(DE3) (bacteria)469008
65Escherichia coli BL21(DE3) (bacteria)469008
106Escherichia coli DH5[alpha] (bacteria)668369
117Escherichia coli DH5[alpha] (bacteria)668369
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
12.5 mMsodium chlorideNaClSodium chloride1
210 mMTris1
32 mMEthylenediaminetetraacetic acidEDTAEthylenediaminetetraacetic acid1
45 mM2-mercaptoethanolBME1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono-disperse.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: blot for 4.5 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 92000 X / Calibrated magnification: 123811 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 33 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 1950

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1.14CTF correction
7RELION3.1.0model fitting
9RELION3.1.0initial Euler assignment
10RELION3.1.0final Euler assignment
11RELION3.1.0classification
12RELION3.1.03D reconstruction
13PHENIX1.15.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 127778
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42826 / Algorithm: BACK PROJECTION / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: rmsd
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
11F66

1f66

A1
21F66

1f66

B1
31F66

1f66

C1
41F66

1f66

D1
51F66

1f66

E1
61F66

1f66

F1
71F66

1f66

G1
81F66

1f66

H1
96FQ5

6fq5

I1
106FQ5

6fq5

J1
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00712230
ELECTRON MICROSCOPYf_angle_d0.75717678
ELECTRON MICROSCOPYf_dihedral_angle_d24.3386410
ELECTRON MICROSCOPYf_chiral_restr0.0422019
ELECTRON MICROSCOPYf_plane_restr0.0221425

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