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- PDB-6t7c: Structure of two copies of human Sox11 transcription factor in co... -

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Basic information

Entry
Database: PDB / ID: 6t7c
TitleStructure of two copies of human Sox11 transcription factor in complex with a nucleosome
Components
  • (DNA (147-MER)) x 2
  • Histone H2A type 1-B/E
  • Histone H2B type 1-K
  • Histone H3.2
  • Histone H4
  • Transcription factor SOX-11
KeywordsNUCLEAR PROTEIN / Nucleosome / DNA / histones / Sox11 / transcription factor / pioneer factor
Function / homology
Function and homology information


positive regulation of lens epithelial cell proliferation / cell cycle checkpoint signaling => GO:0000075 / closure of optic fissure / noradrenergic neuron differentiation / soft palate development / cornea development in camera-type eye / positive regulation of hippo signaling / cardiac ventricle formation / negative regulation of lymphocyte proliferation / glial cell development ...positive regulation of lens epithelial cell proliferation / cell cycle checkpoint signaling => GO:0000075 / closure of optic fissure / noradrenergic neuron differentiation / soft palate development / cornea development in camera-type eye / positive regulation of hippo signaling / cardiac ventricle formation / negative regulation of lymphocyte proliferation / glial cell development / neural tube formation / lens morphogenesis in camera-type eye / hard palate development / glial cell proliferation / embryonic skeletal system morphogenesis / negative regulation of glial cell proliferation / negative regulation of transcription regulatory region DNA binding / somite development / limb bud formation / embryonic digestive tract morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / sympathetic nervous system development / neuroepithelial cell differentiation / neural crest cell development / positive regulation of ossification / positive regulation of hormone secretion / positive regulation of stem cell proliferation / positive regulation of BMP signaling pathway / positive regulation of neurogenesis / skeletal muscle cell differentiation / lung morphogenesis / oligodendrocyte development / ventricular septum morphogenesis / spinal cord development / outflow tract morphogenesis / eyelid development in camera-type eye / negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / anatomical structure morphogenesis / DNA replication-independent nucleosome assembly / positive regulation of osteoblast differentiation / telomere capping / interleukin-7-mediated signaling pathway / negative regulation of cell death / chromatin silencing / telomere organization / DNA replication-dependent nucleosome assembly / innate immune response in mucosa / nucleosome => GO:0000786 / rDNA heterochromatin assembly / negative regulation of gene expression, epigenetic / regulation of gene silencing by miRNA / nuclear chromosome / DNA-templated transcription, initiation / positive regulation of neuron differentiation / skeletal system development / regulation of megakaryocyte differentiation / neuron differentiation / nucleosome assembly / nucleosome / kidney development / double-strand break repair via nonhomologous end joining / chromatin organization / chromosome, telomeric region => GO:0000781 / killing of cells of other organism / DNA-binding transcription activator activity, RNA polymerase II-specific / antibacterial humoral response / transcription cis-regulatory region binding / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / protein ubiquitination / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / defense response to Gram-negative bacterium / protein heterodimerization activity / negative regulation of gene expression / defense response to Gram-positive bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / chromatin => GO:0000785 / protein domain specific binding / DNA-binding transcription factor activity / cellular protein metabolic process / regulation of transcription, DNA-templated / positive regulation of gene expression / positive regulation of cell population proliferation / positive regulation of transcription, DNA-templated / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / nucleoplasm / nucleus / cytosol
Histone H2B / Transcription factor SOX-11 / Transcription factor SOX-12/11/4 / Histone-fold / Histone H4 / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / High mobility group box domain superfamily / High mobility group box domain ...Histone H2B / Transcription factor SOX-11 / Transcription factor SOX-12/11/4 / Histone-fold / Histone H4 / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / High mobility group box domain superfamily / High mobility group box domain / Histone H2A/H2B/H3 / TATA box binding protein associated factor (TAF) / Histone H4, conserved site / Histone H3/CENP-A / Histone H2A / High mobility group box domain / DNA Binding (I), subunit A / Histone, subunit A / Histone, subunit A / Orthogonal Bundle / Mainly Alpha
Histone H2B type 1-K / Histone H2A type 1-B/E / Transcription factor SOX-11 / Histone H4 / Histone H3.2
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsDodonova, S.O. / Zhu, F. / Dienemann, C. / Taipale, J. / Cramer, P.
Funding support Germany, 3items
OrganizationGrant numberCountry
European Research Council (ERC)693023 Germany
European Molecular Biology Organization (EMBO)ALTF-949-2016 Germany
Volkswagen Foundation Germany
CitationJournal: Nature / Year: 2020
Title: Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.
Authors: Svetlana O Dodonova / Fangjie Zhu / Christian Dienemann / Jussi Taipale / Patrick Cramer /
Abstract: 'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions ...'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

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Structure viewerMolecule:
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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 (147-MER)
J: DNA (147-MER)
K: Transcription factor SOX-11
L: Transcription factor SOX-11


Theoretical massNumber of molelcules
Total (without water)231,26312
Polymers231,26312
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 10 molecules AEBFCGDHKL

#1: Protein Histone H3.2 / Histone H3/m / Histone H3/o


Mass: 15389.036 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST2H3A, HIST2H3C, H3F2, H3FM, HIST2H3D / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: Q71DI3
#2: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 16707.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Plasmid: LIC-1B (MacroLabs) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: P04908
#4: Protein Histone H2B type 1-K / H2B K / HIRA-interacting protein 1


Mass: 13921.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BK, H2BFT, HIRIP1 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: O60814
#7: Protein Transcription factor SOX-11


Mass: 12856.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOX11 / Plasmid: LIC-1B (MacroLabs) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: P35716

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (147-MER)


Mass: 45240.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (147-MER)


Mass: 45484.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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
IDNameTypeEntity IDParent-IDSource
1Structure of two copies of human Sox11 transcription factor in complex with a nucleosomeCOMPLEX#1-#70MULTIPLE SOURCES
2Histones and Sox11COMPLEX#1-#4, #71RECOMBINANT
3DNACOMPLEX#5-#61RECOMBINANT
Molecular weightValue: 0.229 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli BL21(DE3) (bacteria)469008
33synthetic construct (others)32630
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
230 mMNaClSodium chloride1
31 mMEDTAEthylenediaminetetraacetic acid1
42 mMDTT1
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 0.39 mB, 25 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K
Details: The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen ...Details: The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: At least 50% of the data were collected at 25* stage tilt in order to partially compensate for preferred orientation of particles on the grid, and to improve angular distribution.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.125 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV
Image scansMovie frames/image: 40

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Processing

EM software
IDNameCategory
2EPUimage acquisition
4GctfCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109666 / Symmetry type: POINT
EM volume selectionDetails: 1733 vesicles and near-complete buds were picked from 61 tomograms. Subtomograms were extracted from the surface of the vesicles.
Num. of tomograms: 54 / Num. of volumes extracted: 2547
Atomic model buildingB value: 130 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 6FQ5

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