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- EMDB-74113: Competition for different elements of the nucleosome acidic patch... -

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Basic information

Entry
Database: EMDB / ID: EMD-74113
TitleCompetition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2
Map data
Sample
  • Complex: Nucleosome-VHH complex containing single-chain antibody 1B2
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • DNA: DNA Tracking Strand
    • DNA: DNA lagging strand
    • Protein or peptide: Single-chain antibody (VHH) 1B2
Keywordschromatin / nucleosome / VHH / antibody / acidic-patch / AP / DE NOVO PROTEIN
Function / homology
Function and homology information


ChAHP complex assembly / Interaction of NuRD complexes with transcription factors / FXIIa activates plasma kallikrein-kinin system / NuRD complex assembly / CHD6, CHD7, CHD8, CHD9 subfamily / CHD1 and CHD2 subfamily / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus ...ChAHP complex assembly / Interaction of NuRD complexes with transcription factors / FXIIa activates plasma kallikrein-kinin system / NuRD complex assembly / CHD6, CHD7, CHD8, CHD9 subfamily / CHD1 and CHD2 subfamily / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / Interleukin-7 signaling / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Meiotic synapsis / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Transcriptional regulation by small RNAs / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosomal DNA binding / RMTs methylate histone arginines / Metalloprotease DUBs / HCMV Early Events / innate immune response in mucosa / structural constituent of chromatin / nucleosome / Regulation of PD-L1(CD274) transcription / UCH proteinases / nucleosome assembly / HATs acetylate histones / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Dengue Virus-Host Interactions / antimicrobial humoral immune response mediated by antimicrobial peptide / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / killing of cells of another organism / chromatin organization / heterochromatin formation / defense response to Gram-negative bacterium / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / negative regulation of cell population proliferation / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / : / DNA binding / RNA binding / extracellular exosome / nucleoplasm / extracellular region / membrane / nucleus
Similarity search - Function
: / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2A conserved site / Histone H2A signature. / 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
Similarity search - Domain/homology
Histone H2B type 1-K / Histone H2A type 1-B/E / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human) / artificial sequences (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsChakraborty U / Saccone EC / Becerra GC / Khan LF / Arslanovic N / Aguilar R / Gloor SL / Hunt SR / Folkwein HJ / Husby NL ...Chakraborty U / Saccone EC / Becerra GC / Khan LF / Arslanovic N / Aguilar R / Gloor SL / Hunt SR / Folkwein HJ / Husby NL / Maier KE / Marunde MR / Schomburg NK / Vaidya A / Cowles MW / Venters BJ / Kassavetis G / Sun Z-W / Kadonaga JT / Armache J-P / Keogh M-C / Tyler JK
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R44HG010640 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R44GM117683 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R44GM136172 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R44CA212733 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R43GM134834 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM149780 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM139816 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA95641 United States
CitationJournal: bioRxiv / Year: 2026
Title: Different modes of engagement with the nucleosome acidic patch yield distinct functional outcomes.
Authors: Ujani Chakraborty / Emma Christina Saccone / Grisel Cruz-Becerra / Laiba F Khan / Nina Arslanovic / Rhiannon Aguilar / Susan L Gloor / Sabrina R Hunt / Heather J Folkwein / Natalia Ledo ...Authors: Ujani Chakraborty / Emma Christina Saccone / Grisel Cruz-Becerra / Laiba F Khan / Nina Arslanovic / Rhiannon Aguilar / Susan L Gloor / Sabrina R Hunt / Heather J Folkwein / Natalia Ledo Husby / Keith E Maier / Matthew R Marunde / Noah K Schomburg / Anup Vaidya / Martis W Cowles / Bryan J Venters / George Kassavetis / Zu-Wen Sun / James T Kadonaga / Jean-Paul Armache / Michael-Christopher Keogh / Jessica K Tyler /
Abstract: The nucleosome acidic patch is a hub of coordinated engagement by proteins that regulate genomic function. Here we report that Dot5 contains an arginine-rich HMGN-like motif that mediates nucleosome ...The nucleosome acidic patch is a hub of coordinated engagement by proteins that regulate genomic function. Here we report that Dot5 contains an arginine-rich HMGN-like motif that mediates nucleosome acidic patch binding and is required for the cell growth, DNA repair and heterochromatin defects exhibited when the protein is overexpressed. The heterologous expression of camelid single chain antibodies to the nucleosome acidic patch confers a similar range of phenotypes, with the most severe observed when an 'arginine-anchor' mode of binding analogous to many endogenous factors is employed. This highlights a delicate balance between nucleosome acidic patch interactors critical for normal cellular functions and dysregulated in disease.
History
DepositionNov 30, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74113.png

Downloads & links

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Map

FileDownload / File: emd_74113.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 329.34 Å		1.1 Å/pix.
x 300 pix.
= 329.34 Å		1.1 Å/pix.
x 300 pix.
= 329.34 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0978 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.27502668 - 0.8944439
Average (Standard dev.)-0.00065213785 (±0.018334722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 329.34 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: auto-sharpened with -50 bfactor

Fileemd_74113_additional_1.map
Annotationauto-sharpened with -50 bfactor
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74113_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74113_half_map_2.map
Projections & Slices
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Sample components

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Entire : Nucleosome-VHH complex containing single-chain antibody 1B2

EntireName: Nucleosome-VHH complex containing single-chain antibody 1B2
Components
  • Complex: Nucleosome-VHH complex containing single-chain antibody 1B2
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • DNA: DNA Tracking Strand
    • DNA: DNA lagging strand
    • Protein or peptide: Single-chain antibody (VHH) 1B2

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Supramolecule #1: Nucleosome-VHH complex containing single-chain antibody 1B2

SupramoleculeName: Nucleosome-VHH complex containing single-chain antibody 1B2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 KDa

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.433398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQSS AVMALQEACE AYLVGLFEDT NLCAIHAKRV TIMPKDIQL ARRIRGER

UniProtKB: Histone H3.2

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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: Homo sapiens (human)
Molecular weightTheoretical: 8.910394 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DNIQGITKPA IRRLARRGGV KRISGLIYEE TRGVLKVFLE NVIRDAVTYT EHAKRKTVTA MDVVYALKRQ GRTLYGFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.167232 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLG RVTIAQGGVL PNIQAVLLPK KT

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.362902 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RKESYSVYVY KVLKQVHPDT GISSKAMGIM NSFVNDIFER IAGEASRLAH YNKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKY TSAK

UniProtKB: Histone H2B type 1-K

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Macromolecule #7: Single-chain antibody (VHH) 1B2

MacromoleculeName: Single-chain antibody (VHH) 1B2 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: artificial sequences (others)
Molecular weightTheoretical: 13.149592 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGG SVQPGGSLKL TCAASRSIFR FAERSTEWYR QAVGKQRELV AAIMSGGTTN YADSVKGRFT ISRDNAKSTI YLQMNSLKS EDTAVYYCHV QEYGRVWSDH WGQGTQVTVS

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Macromolecule #5: DNA Tracking Strand

MacromoleculeName: DNA Tracking Strand / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: artificial sequences (others)
Molecular weightTheoretical: 44.520383 KDa
SequenceString: (DA)(DT)(DC)(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) ...String:
(DA)(DT)(DC)(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)(DG) (DA)(DT)

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Macromolecule #6: DNA lagging strand

MacromoleculeName: DNA lagging strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: artificial sequences (others)
Molecular weightTheoretical: 44.99166 KDa
SequenceString: (DA)(DT)(DC)(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) ...String:
(DA)(DT)(DC)(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)(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

Concentration1.3 mg/mL
BufferpH: 7.6
Details: 20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 10279 / 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 / Nominal defocus max: 2.2 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: 12716462
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 276423
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.7)
Final 3D classificationNumber classes: 1
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3lz0

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9zen:
Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2

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