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- EMDB-17183: OCT4 and MYC-MAX co-bound to a nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-17183
TitleOCT4 and MYC-MAX co-bound to a nucleosome
Map dataSharpened map (LocScale)
Sample
  • Complex: MYC-MAX and OCT4-bound nucleosome
    • Complex: Nucleosomal core particle
      • Complex: Histone octamer
        • Protein or peptide: Histone H3.1
        • Protein or peptide: Histone H4
        • Protein or peptide: Histone H2A type 1-B/E
        • Protein or peptide: Histone H2B type 1-J
      • Complex: Nucleosomal DNA
        • DNA: DNA (127-MER)
        • DNA: DNA (127-MER)
    • Complex: Nucleosome-bound factors
      • Complex: OCT4
        • Protein or peptide: Green fluorescent protein,POU domain, class 5, transcription factor 1
      • Complex: cMYC-MAX heterodimer
        • Protein or peptide: Myc proto-oncogene protein
        • Protein or peptide: Protein max
  • Ligand: PENTANEDIAL
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


Mad-Max complex / cell fate commitment involved in formation of primary germ layer / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / cardiac cell fate determination / Myc-Max complex ...Mad-Max complex / cell fate commitment involved in formation of primary germ layer / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / cardiac cell fate determination / Myc-Max complex / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / cellular response to interferon-alpha / RNA polymerase II transcription repressor complex / heart induction / myotube differentiation / positive regulation of B cell apoptotic process / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / RUNX3 regulates WNT signaling / Specification of primordial germ cells / Specification of the neural plate border / TFAP2 (AP-2) family regulates transcription of cell cycle factors / Transcriptional regulation of pluripotent stem cells / negative regulation of cell division / negative regulation of monocyte differentiation / Germ layer formation at gastrulation / detection of mechanical stimulus involved in sensory perception of sound / response to growth factor / response to alkaloid / B cell apoptotic process / transcription regulator activator activity / protein-DNA complex disassembly / Transcription of E2F targets under negative control by DREAM complex / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / miRNA binding / regulation of telomere maintenance / positive regulation of mesenchymal cell proliferation / middle ear morphogenesis / skeletal system morphogenesis / Signaling by ALK / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / pigmentation / rRNA metabolic process / Transcriptional Regulation by E2F6 / E-box binding / positive regulation of telomere maintenance / MLL1 complex / skeletal muscle cell differentiation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / blastocyst development / somatic stem cell population maintenance / anatomical structure morphogenesis / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of transcription initiation by RNA polymerase II / chromosome organization / BMP signaling pathway / negative regulation of fibroblast proliferation / core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / Cyclin E associated events during G1/S transition / protein localization to CENP-A containing chromatin / Cyclin A:Cdk2-associated events at S phase entry / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / ERK1 and ERK2 cascade / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / negative regulation of miRNA transcription / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / bioluminescence / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / positive regulation of epithelial cell proliferation / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / : / Homeobox, conserved site / 'Homeobox' domain signature. / Helix-loop-helix DNA-binding domain / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / : / 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 / Homeobox-like domain superfamily / 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
Myc proto-oncogene protein / Histone H2A type 1-B/E / Histone H2B type 1-J / Green fluorescent protein / Protein max / Histone H4 / Histone H3.1 / POU domain, class 5, transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMichael AK / Stoos L / Kempf G / Cavadini S / Thoma N
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 21, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17183.png

Downloads & links

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Map

FileDownload / File: emd_17183.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map (LocScale)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.116
Minimum - Maximum-0.25934097 - 0.6668743
Average (Standard dev.)0.0036975069 (±0.025109285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened full map

Fileemd_17183_additional_1.map
AnnotationUnsharpened full map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_17183_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_17183_half_map_2.map
AnnotationHalf map B
Projections & Slices
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Slices (1/2)
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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: Nucleosomal core particle
      • Complex: Histone octamer
        • Protein or peptide: Histone H3.1
        • Protein or peptide: Histone H4
        • Protein or peptide: Histone H2A type 1-B/E
        • Protein or peptide: Histone H2B type 1-J
      • Complex: Nucleosomal DNA
        • DNA: DNA (127-MER)
        • DNA: DNA (127-MER)
    • Complex: Nucleosome-bound factors
      • Complex: OCT4
        • Protein or peptide: Green fluorescent protein,POU domain, class 5, transcription factor 1
      • Complex: cMYC-MAX heterodimer
        • Protein or peptide: Myc proto-oncogene protein
        • Protein or peptide: Protein max
  • Ligand: PENTANEDIAL

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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: #1-#9

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Supramolecule #2: Nucleosomal core particle

SupramoleculeName: Nucleosomal core particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6

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Supramolecule #3: Histone octamer

SupramoleculeName: Histone octamer / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Nucleosomal DNA

SupramoleculeName: Nucleosomal DNA / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Supramolecule #5: Nucleosome-bound factors

SupramoleculeName: Nucleosome-bound factors / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #7-#9

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Supramolecule #6: OCT4

SupramoleculeName: OCT4 / type: complex / ID: 6 / Parent: 5 / Macromolecule list: #7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: cMYC-MAX heterodimer

SupramoleculeName: cMYC-MAX heterodimer / type: complex / ID: 7 / Parent: 5 / Macromolecule list: #8-#9
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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.719445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

UniProtKB: Histone H3.1

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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: Homo sapiens (human)
Molecular weightTheoretical: 11.676703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

UniProtKB: Histone H4

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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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.447825 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.088336 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSA

UniProtKB: Histone H2B type 1-J

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Macromolecule #7: Green fluorescent protein,POU domain, class 5, transcription factor 1

MacromoleculeName: Green fluorescent protein,POU domain, class 5, transcription factor 1
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.81441 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTY GVQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY KTRAEVKFEG DTLVNRIELK GIDFKEDGNI L GHKLEYNY ...String:
MDWSHPQFEK SAVDENLYFQ GGMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTY GVQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY KTRAEVKFEG DTLVNRIELK GIDFKEDGNI L GHKLEYNY NSHNVYIMAD KQKNGIKVNF KIRHNIEDGS VQLADHYQQN TPIGDGPVLL PDNHYLSTQS KLSKDPNEKR DH MVLLEFV TAAGITLGMD ELYKEAAAKE AAAKMAGHLA SDFAFSPPPG GGGDGPGGPE PGWVDPRTWL SFQGPPGGPG IGP GVGPGS EVWGIPPCPP PYEFCGGMAY CGPQVGVGLV PQGGLETSQP EGEAGVGVES NSDGASPEPC TVTPGAVKLE KEKL EQNPE ESQDIKALQK ELEQFAKLLK QKRITLGYTQ ADVGLTLGVL FGKVFSQTTI CRFEALQLSF KNMCKLRPLL QKWVE EADN NENLQEICKA ETLVQARKRK RTSIENRVRG NLENLFLQCP KPTLQQISHI AQQLGLEKDV

UniProtKB: Green fluorescent protein, POU domain, class 5, transcription factor 1

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Macromolecule #8: Myc proto-oncogene protein

MacromoleculeName: Myc proto-oncogene protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.501192 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHEEN VKRRTHNVLE RQRRNELKRS FFALRDQIPE LENNEKAPKV VILKKATAYI LSVQAEEQKL ISEEDLLRKR REQLKHKLE QLRNS

UniProtKB: Myc proto-oncogene protein

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Macromolecule #9: Protein max

MacromoleculeName: Protein max / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.780037 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADKRAHHNA LERKRRDHIK DSFHSLRDSV PSLQGEKASR AQILDKATEY IQYMRRKNHT HQQDIDDLKR QNALLEQQVR AL

UniProtKB: Protein max

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Macromolecule #5: DNA (127-MER)

MacromoleculeName: DNA (127-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 39.092895 KDa
SequenceString: (DC)(DT)(DT)(DT)(DG)(DT)(DT)(DA)(DT)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(DG)(DG)(DG)(DG) (DT)(DG)(DG)(DG)(DG)(DC)(DG)(DT)(DC) (DG)(DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT) (DC) (DT)(DA)(DG)(DC)(DA)(DC) ...String:
(DC)(DT)(DT)(DT)(DG)(DT)(DT)(DA)(DT)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(DG)(DG)(DG)(DG) (DT)(DG)(DG)(DG)(DG)(DC)(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)(DC)(DT) (DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG) (DC)(DA)(DC)(DG)(DT) (DG)(DT)(DC)(DA) (DG)(DA)(DT)

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Macromolecule #6: DNA (127-MER)

MacromoleculeName: DNA (127-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 39.298047 KDa
SequenceString: (DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG) (DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT) (DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG) (DG) (DC)(DG)(DG)(DT)(DT)(DA) ...String:
(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG) (DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT)(DA)(DG)(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)(DG)(DC)(DC)(DC) (DC)(DA)(DC)(DC)(DC)(DC)(DG)(DA)(DT)(DT) (DT)(DG)(DC)(DA)(DT) (DA)(DA)(DC)(DA) (DA)(DA)(DG)

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Macromolecule #10: PENTANEDIAL

MacromoleculeName: PENTANEDIAL / type: ligand / ID: 10 / Number of copies: 8 / Formula: PTD
Molecular weightTheoretical: 100.116 Da
Chemical component information

ChemComp-PTD:
PENTANEDIAL

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102411
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
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
Output model

PDB-8ots:
OCT4 and MYC-MAX co-bound to a nucleosome

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