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- EMDB-71726: nucleosome containing histone variant macroH2A -

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Basic information

Entry
Database: EMDB / ID: EMD-71726
Titlenucleosome containing histone variant macroH2A
Map data
Sample
  • Complex: nucleosome containing histone variant macroH2A
    • Protein or peptide: Core histone macro-H2A.1
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • DNA: DNA Widom601 (208bp) strand1
    • DNA: DNA Widom601 (208bp) strand2
    • Protein or peptide: scFv20
Keywordscomplex / histone / DNA / nucleosome / chromatin / DNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / double-stranded methylated DNA binding ...negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / double-stranded methylated DNA binding / positive regulation of endodermal cell differentiation / regulation of oxidative phosphorylation / establishment of protein localization to chromatin / Barr body / sex chromatin / rDNA binding / dosage compensation by inactivation of X chromosome / poly-ADP-D-ribose modification-dependent protein binding / positive regulation of keratinocyte differentiation / negative regulation of response to oxidative stress / nucleosomal DNA binding / protein poly-ADP-ribosylation / nuclear chromosome / negative regulation of gene expression, epigenetic / regulation of lipid metabolic process / protein serine/threonine kinase inhibitor activity / pericentric heterochromatin / site of DNA damage / condensed chromosome / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / heterochromatin formation / chromosome, telomeric region / transcription cis-regulatory region binding / protein heterodimerization activity / DNA repair / protein kinase binding / chromatin / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
Core histone macro-H2A / Core histone macro-H2A, macro domain / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...Core histone macro-H2A / Core histone macro-H2A, macro domain / : / Histone H2B 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 / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
Core histone macro-H2A.1 / Histone H2B 1.1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / Mus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTan D / Sokolova V
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1942049 United States
CitationJournal: To Be Published
Title: nucleosome containing histone variant macroH2A
Authors: Tan D / Sokolova V
History
DepositionJul 16, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71726.png

Downloads & links

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Map

FileDownload / File: emd_71726.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.)
0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0206
Minimum - Maximum-0.12708396 - 0.24331684
Average (Standard dev.)0.00033634185 (±0.0070414147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71726_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71726_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 variant macroH2A

EntireName: nucleosome containing histone variant macroH2A
Components
  • Complex: nucleosome containing histone variant macroH2A
    • Protein or peptide: Core histone macro-H2A.1
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • DNA: DNA Widom601 (208bp) strand1
    • DNA: DNA Widom601 (208bp) strand2
    • Protein or peptide: scFv20

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Supramolecule #1: nucleosome containing histone variant macroH2A

SupramoleculeName: nucleosome containing histone variant macroH2A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: human histone variant macroH2A containing the histone fold and the linker domains
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Core histone macro-H2A.1

MacromoleculeName: Core histone macro-H2A.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.2516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSSRGGKKKS TKTSRSAKAG VIFPVGRMLR YIKKGHPKYR IGVGAPVYMA AVLEYLTAEI LELAGNAARD NKKGRVTPRH ILLAVANDE ELNQLLKGVT IASGGVLPNI HPELLAKKRG SKGKLEAIIT PPPAKKAKSP SQKKPVSKKA GGKKGARKSK K K

UniProtKB: Core histone macro-H2A.1

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Macromolecule #2: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.848097 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #3: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #7: scFv20

MacromoleculeName: scFv20 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.34542 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV ...String:
MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV KMPCKASGYT FTSYTIQWVK QTPRQGLEWI GYIYPYNAGT KYNEKFKGKA TLTSDKSSST VYMELSSLTS ED SAVYYCA RKSSRLRSTL DYWGQGTSVT VSS

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Macromolecule #5: DNA Widom601 (208bp) strand1

MacromoleculeName: DNA Widom601 (208bp) strand1 / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 63.988711 KDa
SequenceString: (DA)(DC)(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) ...String:
(DA)(DC)(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)(DT)(DG)(DC) (DA) (DT)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DA)(DC) (DA)(DG)(DC)(DG)(DA)(DC)(DC)(DT)(DT) (DG)(DC)(DC)(DG)(DG)(DA)(DG)(DT)

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Macromolecule #6: DNA Widom601 (208bp) strand2

MacromoleculeName: DNA Widom601 (208bp) strand2 / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 64.456039 KDa
SequenceString: (DA)(DC)(DT)(DC)(DC)(DG)(DG)(DC)(DA)(DA) (DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT) (DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DC) ...String:
(DA)(DC)(DT)(DC)(DC)(DG)(DG)(DC)(DA)(DA) (DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT) (DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG) (DC)(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)(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)(DG)(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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 4 / Average exposure time: 2.27 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 81000
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

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: The AlphaFold3 predicted structure of mH2A nucleosome, the PDB model of scFv (PDB: 7k5x), and the DNA from PDB model(PDB: 3lz0) were combined and used to generate the initial model.
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 200000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: EMAN2
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 5.0)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9pm0:
nucleosome containing histone variant macroH2A

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