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- EMDB-77248: canonical nucleosome in complex with scFv antibodies -

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Basic information

Entry
Database: EMDB / ID: EMD-77248
Titlecanonical nucleosome in complex with scFv antibodies
Map data
Sample
  • Complex: canonical nucleosome in complex with scFv antibodies
    • Protein or peptide: canonical histone H2A
    • Protein or peptide: Canonical histone H3
    • Protein or peptide: canonical histone H2B
    • Protein or peptide: canonical histone H4
    • Protein or peptide: scFv antibody
Keywordscomplex / histone / DNA / nucleosome / chromatin / DNA BINDING PROTEIN
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / heterochromatin formation / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Biological speciesXenopus laevis (African clawed frog) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsTan D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1942049 United States
CitationJournal: To Be Published
Title: Canonical nucleosome in complex with scFv antibodies
Authors: Tan D
History
DepositionMay 20, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77248.png

Downloads & links

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Map

FileDownload / File: emd_77248.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.)
1.12 Å/pix.
x 256 pix.
= 286.72 Å		1.12 Å/pix.
x 256 pix.
= 286.72 Å		1.12 Å/pix.
x 256 pix.
= 286.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0106
Minimum - Maximum-0.013385533 - 0.026719118
Average (Standard dev.)-0.000046509245 (±0.0009762301)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 286.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77248_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_77248_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_77248_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 : canonical nucleosome in complex with scFv antibodies

EntireName: canonical nucleosome in complex with scFv antibodies
Components
  • Complex: canonical nucleosome in complex with scFv antibodies
    • Protein or peptide: canonical histone H2A
    • Protein or peptide: Canonical histone H3
    • Protein or peptide: canonical histone H2B
    • Protein or peptide: canonical histone H4
    • Protein or peptide: scFv antibody

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Supramolecule #1: canonical nucleosome in complex with scFv antibodies

SupramoleculeName: canonical nucleosome in complex with scFv antibodies / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: canonical histone H2A

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

UniProtKB: Histone H2A

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Macromolecule #2: Canonical histone H3

MacromoleculeName: Canonical histone H3 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

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Macromolecule #3: canonical histone H2B

MacromoleculeName: canonical histone H2B / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

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Macromolecule #4: canonical histone H4

MacromoleculeName: canonical histone H4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

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Macromolecule #5: scFv antibody

MacromoleculeName: scFv antibody / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 8
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 16 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Average exposure time: 5.0 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / 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
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 122112
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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