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- EMDB-17159: Cryo-EM map of MYC-MAX-OCT4-LIN28 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-17159
TitleCryo-EM map of MYC-MAX-OCT4-LIN28 complex
Map datamap of LIN28-MYC-OCT4 structure
Sample
  • Complex: MYC-MAX and OCT4-bound nucleosome
    • Complex: Histones, human_cMYC and human_MAXHistone
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
      • Protein or peptide: human_cMYC
      • Protein or peptide: human_MAX
    • Complex: OCT4-GFP
      • Protein or peptide: OCT4-GFP
KeywordsTRANSCRIPTION / chromatin
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMichael AK / Kempf G / Cavadini S / Thoma NH
Funding supportEuropean Union, France, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)884331European Union
Human Frontier Science Program (HFSP)LT000646/2018-L5 France
CitationJournal: Nature / Year: 2023
Title: Cooperation between bHLH transcription factors and histones for DNA access.
Authors: Alicia K Michael / Lisa Stoos / Priya Crosby / Nikolas Eggers / Xinyu Y Nie / Kristina Makasheva / Martina Minnich / Kelly L Healy / Joscha Weiss / Georg Kempf / Simone Cavadini / Lukas ...Authors: Alicia K Michael / Lisa Stoos / Priya Crosby / Nikolas Eggers / Xinyu Y Nie / Kristina Makasheva / Martina Minnich / Kelly L Healy / Joscha Weiss / Georg Kempf / Simone Cavadini / Lukas Kater / Jan Seebacher / Luca Vecchia / Deyasini Chakraborty / Luke Isbel / Ralph S Grand / Florian Andersch / Jennifer L Fribourgh / Dirk Schübeler / Johannes Zuber / Andrew C Liu / Peter B Becker / Beat Fierz / Carrie L Partch / Jerome S Menet / Nicolas H Thomä /
Abstract: The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged ...The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. ). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry-exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A-H2B acidic patch, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.
History
DepositionApr 19, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17159.png

Downloads & links

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Map

FileDownload / File: emd_17159.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of LIN28-MYC-OCT4 structure
Voxel sizeX=Y=Z: 0.845 Å
Density
Contour LevelBy AUTHOR: 0.081
Minimum - Maximum-0.23561952 - 0.6414902
Average (Standard dev.)0.007614001 (±0.033512067)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map of LIN28-MYC-OCT4 structure

Fileemd_17159_half_map_1.map
Annotationhalf map of LIN28-MYC-OCT4 structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of LIN28-MYC-OCT4 structure

Fileemd_17159_half_map_2.map
Annotationhalf map of LIN28-MYC-OCT4 structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MYC-MAX and OCT4-bound nucleosome

EntireName: MYC-MAX and OCT4-bound nucleosome
Components
  • Complex: MYC-MAX and OCT4-bound nucleosome
    • Complex: Histones, human_cMYC and human_MAXHistone
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
      • Protein or peptide: human_cMYC
      • Protein or peptide: human_MAX
    • Complex: OCT4-GFP
      • Protein or peptide: OCT4-GFP

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Supramolecule #1: MYC-MAX and OCT4-bound nucleosome

SupramoleculeName: MYC-MAX and OCT4-bound nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Histones, human_cMYC and human_MAX

SupramoleculeName: Histones, human_cMYC and human_MAX / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: OCT4-GFP

SupramoleculeName: OCT4-GFP / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAC EAYLVGLFED TNLCAIHAKR VTIMPKDIQL ARRIRGERA

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMDV VYALKRQGRT LYGFGG

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQLA IRNDEELNKL LGRVTIAQGG VLPNIQAVLL PKKTESHHKA KGK

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNKR STITSREIQT AVRLLLPGEL AKHAVSEGTK AVTKYTSA

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Macromolecule #5: human_cMYC

MacromoleculeName: human_cMYC / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHEEN VKRRTHNVLE RQRRNELKRS FFALRDQIPE LENNEKAPKV VILKKATAYI LSVQAEEQKL ISEEDLLRKR REQLKHKLEQ LRNS

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Macromolecule #6: human_MAX

MacromoleculeName: human_MAX / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADKRAHHNA LERKRRDHIK DSFHSLRDSV PSLQGEKASR AQILDKATEY IQYMRRKNHT HQQDIDDLKR QNALLEQQVR AL

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Macromolecule #7: OCT4-GFP

MacromoleculeName: OCT4-GFP / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLEYNYNS ...String:
MDWSHPQFEK SAVDENLYFQ GGMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLEYNYNS HNVYIMADKQ KNGIKVNFKI RHNIEDGSVQ LADHYQQNTP IGDGPVLLPD NHYLSTQSKL SKDPNEKRDH MVLLEFVTAA GITLGMDELY KEAAAKEAAA KMAGHLASDF AFSPPPGGGG DGPGGPEPGW VDPRTWLSFQ GPPGGPGIGP GVGPGSEVWG IPPCPPPYEF CGGMAYCGPQ VGVGLVPQGG LETSQPEGEA GVGVESNSDG ASPEPCTVTP GAVKLEKEKL EQNPEESQDI KALQKELEQF AKLLKQKRIT LGYTQADVGL TLGVLFGKVF SQTTICRFEA LQLSFKNMCK LRPLLQKWVE EADNNENLQE ICKAETLVQA RKRKRTSIEN RVRGNLENLF LQCPKPTLQQ ISHIAQQLGL EKDV

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17378
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1nkp

source_name: PDB, initial_model_type: experimental model

6t90

source_name: PDB, initial_model_type: experimental model

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