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- EMDB-52852: structure of two human ELF2 transcription factors in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-52852
Titlestructure of two human ELF2 transcription factors in complex with a nucleosome
Map data
Sample
  • Complex: two ELF2 DBD proteins interacting with nucleosome
    • Complex: histone proteins
      • Protein or peptide: histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: transcription factor ELF2
      • Protein or peptide: ETS-related transcription factor Elf-2
    • Complex: DNA
      • DNA: DNA (147-MER)
      • DNA: DNA (147-MER)
Keywordsnucleosome / transcription factor / DNA BINDING PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsXiao T / Crowe-McAuliffe C / Dienemann C / Taipale J
Funding support United Kingdom, Germany, 4 items
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, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52852.png

Downloads & links

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Map

FileDownload / File: emd_52852.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 192 pix.
= 250.368 Å		1.3 Å/pix.
x 192 pix.
= 250.368 Å		1.3 Å/pix.
x 192 pix.
= 250.368 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.304 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0432
Minimum - Maximum-0.028275196 - 0.12945275
Average (Standard dev.)0.0018887686 (±0.0067615733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 250.36801 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: local refinement map

Fileemd_52852_additional_1.map
Annotationlocal refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: half map for local refinement map

Fileemd_52852_additional_2.map
Annotationhalf map for local refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: half map for local refinement map

Fileemd_52852_additional_3.map
Annotationhalf map for local refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: composite map between main map and local refinement map

Fileemd_52852_additional_4.map
Annotationcomposite map between main map and local refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52852_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52852_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : two ELF2 DBD proteins interacting with nucleosome

EntireName: two ELF2 DBD proteins interacting with nucleosome
Components
  • Complex: two ELF2 DBD proteins interacting with nucleosome
    • Complex: histone proteins
      • Protein or peptide: histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: transcription factor ELF2
      • Protein or peptide: ETS-related transcription factor Elf-2
    • Complex: DNA
      • DNA: DNA (147-MER)
      • DNA: DNA (147-MER)

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Supramolecule #1: two ELF2 DBD proteins interacting with nucleosome

SupramoleculeName: two ELF2 DBD proteins interacting with nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: histone proteins

SupramoleculeName: histone proteins / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: transcription factor ELF2

SupramoleculeName: transcription factor ELF2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: histone H3

MacromoleculeName: histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.451192 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

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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: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #5: ETS-related transcription factor Elf-2

MacromoleculeName: ETS-related transcription factor Elf-2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.820217 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TQQSPISNGS PELGIKKKPR EGKGNTTYLW EFLLDLLQDK NTCPRYIKWT QREKGIFKLV DSKAVSKLWG KHKNKPDMNY ETMGRALRY YYQRGILAKV EGQRLVYQFK DMPKNIVVID DDKSETCNED LAGTTDEKSL ERVSLS

UniProtKB: ETS-related transcription factor Elf-2

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Macromolecule #6: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.288875 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DC)(DT)(DG)(DC)(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) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DC)(DT)(DG)(DC)(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)(DG)(DG)(DA)(DA)(DG) (DC)(DG)(DG)(DA)(DA) (DG)(DT)(DT)(DG) (DT)(DA)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)

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Macromolecule #7: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.45798 KDa
SequenceString: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DT)(DA)(DC)(DA)(DA)(DC)(DT)(DT) (DC)(DC)(DG)(DC)(DT)(DT)(DC)(DC)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String:
(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DT)(DA)(DC)(DA)(DA)(DC)(DT)(DT) (DC)(DC)(DG)(DC)(DT)(DT)(DC)(DC)(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)(DG)(DC)(DA)(DG)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(DA)(DG)

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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

BufferpH: 7.5
Details: 1 mM EDTA, 30 mM NaCl, 2 mM DTT in 20 mM HEPES, pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 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 grids imaged: 1 / Number real images: 18283 / Average exposure time: 1.2 sec. / Average electron dose: 51.09 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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: 10450657 / Details: relion template picking
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: CryoSPARC ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 103825
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8ybj

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 137.082
Output model

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

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