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- PDB-9igj: structure of two human ELF2 transcription factors in complex with... -

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Basic information

Entry
Database: PDB / ID: 9igj
Titlestructure of two human ELF2 transcription factors in complex with a nucleosome
Components
  • (DNA (147-MER)) x 2
  • ETS-related transcription factor Elf-2
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H4
  • histone H3
KeywordsDNA BINDING PROTEIN / nucleosome / transcription factor
Function / homology
Function and homology information


RUNX1 regulates transcription of genes involved in BCR signaling / sequence-specific double-stranded DNA binding / structural constituent of chromatin / heterochromatin formation / nucleosome / nucleosome assembly / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / nuclear body ...RUNX1 regulates transcription of genes involved in BCR signaling / sequence-specific double-stranded DNA binding / structural constituent of chromatin / heterochromatin formation / nucleosome / nucleosome assembly / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / nuclear body / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Transcription factor Elf, N-terminal / Transcription factor protein N terminal / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / : ...Transcription factor Elf, N-terminal / Transcription factor protein N terminal / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / : / 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 H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / ETS-related transcription factor Elf-2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsXiao, T. / Crowe-McAuliffe, C. / Dienemann, C. / Taipale, J.
Funding support United Kingdom, Germany, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)G107673 United Kingdom
Cancer Research UKRG99643 United Kingdom
Medical Research Council (MRC, United Kingdom)G105296 United Kingdom
Max Planck Society Germany
CitationJournal: To Be Published
Title: The pioneer transcription factor ELF2 remodels the nucleosome near transcription start sites
Authors: Xiao, T. / Crowe-McAuliffe, C. / Ochmann, M. / Du, Y. / Hou, T. / Chen, Y. / Zhu, F. / Seyednasrollah, F. / Osmala, M. / Vanharanta, S. / Morgunova, E. / Cramer, P. / Rogerson, C. / Dienemann, C. / Taipale, J.
History
DepositionFeb 19, 2025Deposition site: PDBE / Processing site: PDBE
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: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Additional map / Part number: 4 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Part number: 1 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Part number: 2 / 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
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: histone H3
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
L: ETS-related transcription factor Elf-2
K: ETS-related transcription factor Elf-2
J: DNA (147-MER)
I: DNA (147-MER)


Theoretical massNumber of molelcules
Total (without water)233,60912
Polymers233,60912
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 , 5 types, 10 molecules AEBFCGDHLK

#1: Protein histone H3


Mass: 15451.192 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)
#2: Protein Histone H4


Mass: 11394.426 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: 14109.436 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: P06897
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 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: P02281
#5: Protein ETS-related transcription factor Elf-2 / E74-like factor 2 / New ETS-related factor


Mass: 16820.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELF2, NERF / Production host: Escherichia coli (E. coli) / References: UniProt: Q15723

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DNA chain , 2 types, 2 molecules JI

#6: DNA chain DNA (147-MER)


Mass: 45288.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (147-MER)


Mass: 45457.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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
IDNameTypeEntity IDParent-IDSource
1two ELF2 DBD proteins interacting with nucleosomeCOMPLEXall0MULTIPLE SOURCES
2histone proteinsCOMPLEX#1-#41RECOMBINANT
3transcription factor ELF2COMPLEX#51RECOMBINANT
4DNACOMPLEX#6-#71RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Xenopus laevis (African clawed frog)8355
43Homo sapiens (human)9606
54synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562BL21(DE3)
43Escherichia coli (E. coli)562
54synthetic construct (others)32630
Buffer solutionpH: 7.5
Details: 1 mM EDTA, 30 mM NaCl, 2 mM DTT in 20 mM HEPES, pH 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 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: OTHER / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.2 sec. / Electron dose: 51.09 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 18283

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
4WarpCTF correction
7UCSF ChimeraXmodel fitting
9Cootmodel refinement
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10450657 / Details: relion template picking
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103825 / Symmetry type: POINT
Atomic model buildingB value: 137.082 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18YBJ

8ybj

18YBJ1PDBexperimental model
21AlphaFoldin silico model

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