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Basic information

Entry
Database: PDB / ID: 9zen
TitleCompetition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2
Components
  • DNA Tracking Strand
  • DNA lagging strand
  • Histone H2A type 1-B/E
  • Histone H2B type 1-K
  • Histone H3.2
  • Histone H4
  • Single-chain antibody (VHH) 1B2
KeywordsDE NOVO PROTEIN / chromatin / nucleosome / VHH / antibody / acidic-patch / AP
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization ...negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / 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 / innate immune response in mucosa / Defective pyroptosis / Negative Regulation of CDH1 Gene Transcription / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Metalloprotease DUBs / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / structural constituent of chromatin / UCH proteinases / heterochromatin formation / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / killing of cells of another organism / defense response to Gram-negative bacterium / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / chromatin binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
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
DNA / DNA (> 10) / DNA (> 100) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsChakraborty, U. / Saccone, E.C. / Becerra, G.C. / Khan, L.F. / Arslanovic, N. / Aguilar, R. / Gloor, S.L. / Hunt, S.R. / Folkwein, H.J. / Husby, N.L. ...Chakraborty, U. / Saccone, E.C. / Becerra, G.C. / Khan, L.F. / Arslanovic, N. / Aguilar, R. / Gloor, S.L. / Hunt, S.R. / Folkwein, H.J. / Husby, N.L. / Maier, K.E. / Marunde, M.R. / Schomburg, N.K. / Vaidya, A. / Cowles, M.W. / Venters, B.J. / Kassavetis, G. / Sun, Z.-W. / Kadonaga, J.T. / Armache, J.-P. / Keogh, M.-C. / Tyler, J.K.
Funding support United States, 8items
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: To Be Published
Title: Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes
Authors: Chakraborty, U. / Saccone, E.C. / Becerra, G.C. / Khan, L.F. / Arslanovic, N. / Aguilar, R. / Gloor, S.L. / Hunt, S.R. / Folkwein, H.J. / Husby, N.L. / Maier, K.E. / Marunde, M.R. / ...Authors: Chakraborty, U. / Saccone, E.C. / Becerra, G.C. / Khan, L.F. / Arslanovic, N. / Aguilar, R. / Gloor, S.L. / Hunt, S.R. / Folkwein, H.J. / Husby, N.L. / Maier, K.E. / Marunde, M.R. / Schomburg, N.K. / Vaidya, A. / Cowles, M.W. / Venters, B.J. / Kassavetis, G. / Sun, Z.-W. / Kadonaga, J.T. / Armache, J.-P. / Keogh, M.-C. / Tyler, J.K.
History
DepositionNov 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-K
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-K
I: DNA Tracking Strand
J: DNA lagging strand
L: Single-chain antibody (VHH) 1B2
K: Single-chain antibody (VHH) 1B2


Theoretical massNumber of molelcules
Total (without water)201,55912
Polymers201,55912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.2 / H3-clustered histone 13 / H3-clustered histone 14 / H3-clustered histone 15 / Histone H3/m / Histone H3/o


Mass: 11433.398 Da / Num. of mol.: 2 / Mutation: C97S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D
Production host: Escherichia coli (E. coli) / References: UniProt: Q71DI3
#2: Protein Histone H4


Mass: 8910.394 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 12167.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein Histone H2B type 1-K / H2B K / HIRA-interacting protein 1


Mass: 10362.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC12, H2BFT, HIRIP1, HIST1H2BK / Production host: Escherichia coli (E. coli) / References: UniProt: O60814

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA Tracking Strand


Mass: 44520.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial sequences (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA lagging strand


Mass: 44991.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial sequences (others) / Production host: Escherichia coli (E. coli)

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Antibody , 1 types, 2 molecules LK

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


Mass: 13149.592 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial sequences (others) / Production host: Escherichia coli (E. coli)

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Details

Has protein modificationY

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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

ComponentName: Nucleosome-VHH complex containing single-chain antibody 1B2
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.28 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
Details: 20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
SpecimenConc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 10279

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
4cryoSPARC4.7CTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10cryoSPARC4.7initial Euler assignment
11cryoSPARC4.7final Euler assignment
13cryoSPARC4.73D reconstruction
14PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 12716462
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 276423 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13LZ0

3lz0

13LZ01PDBexperimental model
21AlphaFoldin silico model
RefinementHighest resolution: 3.17 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00513664
ELECTRON MICROSCOPYf_angle_d0.78119700
ELECTRON MICROSCOPYf_dihedral_angle_d30.2714148
ELECTRON MICROSCOPYf_chiral_restr0.0432232
ELECTRON MICROSCOPYf_plane_restr0.0071496

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