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- PDB-8ubk: Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome -

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Basic information

Entry
Database: PDB / ID: 8ubk
TitleCryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome
Components
  • (NRCAM DNA (162- ...) x 2
  • Achaete-scute homolog 1
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
  • Transcription factor E2-alpha
  • scFv
KeywordsNUCLEAR PROTEIN / nucleosome / pioneer transcription factors / DNA binding proteins / transcription
Function / homology
Function and homology information


noradrenergic neuron fate commitment / spinal cord oligodendrocyte cell differentiation / spinal cord oligodendrocyte cell fate specification / oligodendrocyte cell fate commitment / regulation of timing of subpallium neuron differentiation / lung neuroendocrine cell differentiation / carotid body glomus cell differentiation / cerebral cortex GABAergic interneuron differentiation / subpallium neuron fate commitment / stomach neuroendocrine cell differentiation ...noradrenergic neuron fate commitment / spinal cord oligodendrocyte cell differentiation / spinal cord oligodendrocyte cell fate specification / oligodendrocyte cell fate commitment / regulation of timing of subpallium neuron differentiation / lung neuroendocrine cell differentiation / carotid body glomus cell differentiation / cerebral cortex GABAergic interneuron differentiation / subpallium neuron fate commitment / stomach neuroendocrine cell differentiation / ventral spinal cord interneuron fate commitment / commitment of neuronal cell to specific neuron type in forebrain / adrenal chromaffin cell differentiation / cellular response to magnetism / parasympathetic nervous system development / vestibular nucleus development / noradrenergic neuron development / musculoskeletal movement, spinal reflex action / olfactory pit development / GABAergic neuron differentiation / spinal cord association neuron differentiation / peripheral nervous system neuron development / neuroblast fate determination / neuroendocrine cell differentiation / regulation of epithelial cell differentiation / bHLH transcription factor binding / neuron fate specification / cell development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / natural killer cell differentiation / motor neuron migration / sympathetic ganglion development / lymphocyte differentiation / regulation of Notch signaling pathway / enteric nervous system development / neuron fate commitment / immunoglobulin V(D)J recombination / sympathetic nervous system development / Peyer's patch development / response to folic acid / Myogenesis / pattern specification process / response to epidermal growth factor / positive regulation of neural precursor cell proliferation / oligodendrocyte development / neural precursor cell proliferation / positive regulation of neurogenesis / generation of neurons / negative regulation of neuron differentiation / B cell lineage commitment / positive regulation of Notch signaling pathway / central nervous system neuron development / E-box binding / oligodendrocyte differentiation / regulation of G1/S transition of mitotic cell cycle / neuroblast proliferation / regulation of neurogenesis / response to retinoic acid / negative regulation of tumor necrosis factor-mediated signaling pathway / neuron development / : / cis-regulatory region sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / cell maturation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / Notch signaling pathway / CENP-A containing nucleosome / positive regulation of B cell proliferation / positive regulation of cell cycle / Packaging Of Telomere Ends / gastrulation / positive regulation of neuron differentiation / 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 / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / regulation of mitotic cell cycle / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / erythrocyte differentiation / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / innate immune response in mucosa / Defective pyroptosis
Similarity search - Function
Achaete-scute transcription factor-related / : / Helix-loop-helix DNA-binding domain / 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 / : / Histone H2B signature. / Histone H2A conserved site ...Achaete-scute transcription factor-related / : / Helix-loop-helix DNA-binding domain / 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 / : / 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 / 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
DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H2B type 1-J / Transcription factor E2-alpha / Histone H4 / Histone H3.1 / Achaete-scute homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhou, B.R. / Bai, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To Be Published
Title: Cryo-EM structure of NRCAM nucleosome aided by scFv
Authors: Zhou, B.R. / Bai, Y.
History
DepositionSep 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 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 H3.1
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: NRCAM DNA (162-MER)
J: NRCAM DNA (162-MER)
M: scFv
N: scFv
O: Achaete-scute homolog 1
P: Transcription factor E2-alpha
Q: Achaete-scute homolog 1
R: Transcription factor E2-alpha


Theoretical massNumber of molelcules
Total (without water)453,65716
Polymers453,65716
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 12 molecules AEBFCGDHOQPR

#1: Protein Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15437.167 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#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
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14165.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 13935.239 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#8: Protein Achaete-scute homolog 1


Mass: 24765.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ascl1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02067
#9: Protein Transcription factor E2-alpha


Mass: 67777.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tcf3 / Production host: Escherichia coli (E. coli) / References: UniProt: P15806

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NRCAM DNA (162- ... , 2 types, 2 molecules IJ

#5: DNA chain NRCAM DNA (162-MER)


Mass: 49865.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#6: DNA chain NRCAM DNA (162-MER)


Mass: 50149.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Antibody , 1 types, 2 molecules MN

#7: Antibody scFv


Mass: 29345.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Details

Has protein modificationY

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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

ComponentName: 162bp NRCAM nucleosome in complex with Ascl1/E12a / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
8PHENIXmodel refinement
13cryoSPARC4.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237174 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00519446
ELECTRON MICROSCOPYf_angle_d0.76427640
ELECTRON MICROSCOPYf_dihedral_angle_d28.3334908
ELECTRON MICROSCOPYf_chiral_restr0.043115
ELECTRON MICROSCOPYf_plane_restr0.0052390

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