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- PDB-9cg9: Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2 -

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Basic information

Entry
Database: PDB / ID: 9cg9
TitleCryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2
Components
  • (Widom 601 DNA ...) x 2
  • High mobility group protein B1
  • Histone H2A type 1
  • Histone H2B
  • Histone H3.2
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / nucleosome / high-mobility group box 1 / HMGB1 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / T-helper 1 cell activation ...: / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / T-helper 1 cell activation / T-helper 1 cell differentiation / positive regulation of myeloid cell differentiation / myeloid dendritic cell activation / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of dendritic cell differentiation / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / positive regulation of glycogen catabolic process / positive regulation of toll-like receptor 4 signaling pathway / DNA geometric change / endothelial cell chemotaxis / RAGE receptor binding / eye development / positive regulation of interleukin-1 production / Regulation of TLR by endogenous ligand / bubble DNA binding / V(D)J recombination / myeloid cell differentiation / alphav-beta3 integrin-HMGB1 complex / myeloid progenitor cell differentiation / Apoptosis induced DNA fragmentation / inflammatory response to antigenic stimulus / macrophage activation involved in immune response / positive regulation of monocyte chemotaxis / positive regulation of monocyte chemotactic protein-1 production / MyD88 deficiency (TLR2/4) / regulation of nucleotide-excision repair / endothelial cell proliferation / positive regulation of vascular endothelial cell proliferation / positive regulation of chemokine (C-X-C motif) ligand 2 production / cellular response to interleukin-7 / glycogen catabolic process / apoptotic cell clearance / IRAK4 deficiency (TLR2/4) / dendritic cell chemotaxis / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of DNA binding / DNA binding, bending / supercoiled DNA binding / positive regulation of wound healing / phosphatidylserine binding / positive regulation of sprouting angiogenesis / chemoattractant activity / endoplasmic reticulum-Golgi intermediate compartment / TRAF6 mediated NF-kB activation / negative regulation of type II interferon production / DNA topological change / Advanced glycosylation endproduct receptor signaling / negative regulation of blood vessel endothelial cell migration / positive regulation of activated T cell proliferation / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / positive regulation of blood vessel endothelial cell migration / Pyroptosis / protein kinase activator activity / four-way junction DNA binding / condensed chromosome / DNA polymerase binding / transcription repressor complex / positive regulation of interleukin-12 production / positive regulation of autophagy / activation of innate immune response / lung development / positive regulation of interferon-beta production / response to glucocorticoid / cytokine activity / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / lipopolysaccharide binding / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / base-excision repair / double-strand break repair via nonhomologous end joining / autophagy / positive regulation of interleukin-6 production / integrin binding / neuron projection development / positive regulation of tumor necrosis factor production / structural constituent of chromatin / transcription corepressor activity / heterochromatin formation / nucleosome / double-strand break repair / nucleosome assembly / single-stranded DNA binding / double-stranded RNA binding / cellular response to lipopolysaccharide
Similarity search - Function
HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / : ...HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A 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 1.1 / Histone H2A type 1 / High mobility group protein B1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsChio, U.S. / Saunders, H.S. / Narlikar, G.J. / Cheng, Y.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127020 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140847 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM137463 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Sci Adv / Year: 2025
Title: HMGB1 deforms nucleosomal DNA to generate a dynamic chromatin environment counteracting the effects of linker histone.
Authors: Hayden S Saunders / Un Seng Chio / Camille M Moore / Vijay Ramani / Yifan Cheng / Geeta J Narlikar /
Abstract: The essential architectural protein HMGB1 increases accessibility of nucleosomal DNA and counteracts the effects of linker histone H1. However, HMGB1 is less abundant than H1 and binds nucleosomes ...The essential architectural protein HMGB1 increases accessibility of nucleosomal DNA and counteracts the effects of linker histone H1. However, HMGB1 is less abundant than H1 and binds nucleosomes more weakly, raising the question of how it competes with H1. Here, we find that HMGB1 increases nucleosomal DNA accessibility without displacing H1. HMGB1 also increases the dynamics of condensed, H1-bound chromatin. Unexpectedly, cryo-electron microscopy structures show HMGB1 bound at internal locations on nucleosomes and local DNA distortion. These sites are away from where H1 binds, explaining how HMGB1 and H1 can co-occupy a nucleosome. Our findings suggest a model where HMGB1 counteracts the effects of H1 by distorting nucleosomal DNA and disrupting interactions of the H1 carboxyl-terminal tail with DNA. Compared to mutually exclusive binding, co-occupancy by HMGB1 and H1 allows greater diversity in dynamic chromatin states. More generally, these results explain how architectural proteins acting at the nucleosome scale can have large effects on chromatin dynamics at the mesoscale.
History
DepositionJun 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half 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
D: Histone H2B
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B
I: Widom 601 DNA reverse strand (147-mer)
J: Widom 601 DNA forward strand (147-mer)
K: High mobility group protein B1


Theoretical massNumber of molelcules
Total (without water)228,24311
Polymers228,24311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3.2


Mass: 15271.863 Da / Num. of mol.: 2 / Mutation: G102A, C110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11263.231 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
#3: Protein Histone H2A type 1


Mass: 13978.241 Da / Num. of mol.: 2 / Mutation: G99R, A123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P06897
#4: Protein Histone H2B / H2B1.1


Mass: 13524.752 Da / Num. of mol.: 2 / Mutation: S32T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P02281
#7: Protein High mobility group protein B1 / High mobility group protein 1 / HMG-1


Mass: 25092.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMGB1, HMG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P09429

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Widom 601 DNA ... , 2 types, 2 molecules IJ

#5: DNA chain Widom 601 DNA reverse strand (147-mer)


Mass: 47746.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 10 base pairs flanking DNA / Source: (synth.) synthetic construct (others)
#6: DNA chain Widom 601 DNA forward strand (147-mer)


Mass: 47328.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 10 base pairs flanking DNA / Source: (synth.) synthetic construct (others)

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Details

Has protein modificationN

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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
IDNameTypeDetailsEntity IDParent-IDSource
1Complex of nucleosome with HMGB1COMPLEXIndividual histones were recombinantly expressed and purified from E. coli BL21(DE3) pLysS as lyopholized powder. Histone octamer was refolded using urea and dialysis and then purified. Widom 601 147-mer DNA with 10 base pairs flanking DNA was generated by PCR. Nucleosome was generated through salt-gradient dialysis of reconstituted histone octamer with DNA. Full-length HMGB1 was recombinantly expressed and purified from E. coli BL21(DE3) Rosetta.all0MULTIPLE SOURCES
20/10 nucleosome with Xenopus laevis histonesCOMPLEXHistones recombinantly expressed in E. coli. DNA generated by PCR.#1-#61MULTIPLE SOURCES
3High mobility group protein B1COMPLEXRecombinantly expressed and purified from E. coli.#71MULTIPLE SOURCES
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.2 MDaNO
210.2 MDaNO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Xenopus laevis (African clawed frog)8355
22Xenopus laevis (African clawed frog)8355
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Escherichia coli BL21(DE3) (bacteria)469008pLysS
22Escherichia coli BL21(DE3) (bacteria)469008pLysS
33Escherichia coli BL21(DE3) (bacteria)469008Rosetta
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
225 mMpotassium chlorideKCl1
31 mMEDTAC10H16N2O81
42 mMDTTC4H10O2S21
51.5 %glycerolC3H8O31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 1 uM nucleosome was mixed with 12 uM HMGB1 prior to plunge freezing.
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K / Details: 3 uL of sample was applied to grid.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.024 sec. / Electron dose: 43 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 8259
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.1.1particle selectionTemplate Picker
4cryoSPARCv4.1.1CTF correction
10cryoSPARC4.1.1initial Euler assignment
11cryoSPARC4.1.1final Euler assignmentNon-uniform Refinement
13cryoSPARC4.1.13D reconstructionNon-uniform Refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42115 / Symmetry type: POINT

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