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- EMDB-42040: Cryo-EM structure of NRCAM nucleosome aided by scFv -

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Basic information

Entry
Database: EMDB / ID: EMD-42040
TitleCryo-EM structure of NRCAM nucleosome aided by scFv
Map data
Sample
  • Complex: 162bp NRCAM nucleosome in complex with scFv
    • 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
    • DNA: NRCAM DNA (162-MER)
    • DNA: NRCAM DNA (162-MER) complementary chain
    • Protein or peptide: scFv20
Keywordsnucleosome / pioneer transcription factors / DNA binding proteins / transcription / NUCLEAR PROTEIN
Function / homology
Function and homology information


negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / epigenetic regulation of gene expression ...negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / epigenetic regulation of gene expression / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Interleukin-7 signaling / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / 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 / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / innate immune response in mucosa / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / Transcriptional regulation by small RNAs / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Negative Regulation of CDH1 Gene Transcription / G2/M DNA damage checkpoint / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / Metalloprotease DUBs / RMTs methylate histone arginines / HCMV Early Events / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome assembly / heterochromatin formation / HATs acetylate histones / antibacterial humoral response / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / killing of cells of another organism / defense response to Gram-negative bacterium / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / : / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
: / 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 ...: / 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 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
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhou BR / Bai Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: Mol Cell / Year: 2026
Title: Distinct associations of pioneer factor Ascl1-E12a with nucleosomes drive changes in cell fate.
Authors: Bing-Rui Zhou / Edgar Luzete-Monteiro / Jingchao Zhang / Naomi Takenaka / Hsin-Yao Tang / Meilin Fernandez Garcia / Mariel Coradin / Megan Frederick / Greg Donahue / Benjamin Garcia / Yawen ...Authors: Bing-Rui Zhou / Edgar Luzete-Monteiro / Jingchao Zhang / Naomi Takenaka / Hsin-Yao Tang / Meilin Fernandez Garcia / Mariel Coradin / Megan Frederick / Greg Donahue / Benjamin Garcia / Yawen Bai / Kenneth S Zaret /
Abstract: Understanding how pioneer transcription factors target nucleosomal DNA and initiate chromatin accessibility reveals the earliest events in cell fate changes. We integrated structural, biochemical, ...Understanding how pioneer transcription factors target nucleosomal DNA and initiate chromatin accessibility reveals the earliest events in cell fate changes. We integrated structural, biochemical, and genomic approaches to assess how the pioneer factor Ascl1-E12a heterodimer perturbs nucleosomes in vitro and in vivo to induce a neural cell fate. Two Ascl1-E12a heterodimers shift and unwrap 15 bp of nucleosomal DNA in a stepwise manner while eliciting solvent exchanges within the octamer. Nucleosome binding, but not free DNA binding, by Ascl1-E12a is enhanced by two types of associations with the nucleosome that differentially affect the kinetics of DNA unwrapping and shifting. Nucleosome association mutants of Ascl1 perturb chromatin opening on linker histone-compacted nucleosome arrays-independent of nucleosome remodelers-and targeting of closed chromatin in vivo, with consequent deficiencies in cellular reprogramming. Our findings establish that distinct associations with nucleosomes are essential for the pioneer factor Ascl1 to overcome chromatin barriers to reprogram cell fate.
History
DepositionSep 20, 2023-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42040.png

Downloads & links

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Map

FileDownload / File: emd_42040.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 320 pix.
= 325.248 Å		1.02 Å/pix.
x 320 pix.
= 325.248 Å		1.02 Å/pix.
x 320 pix.
= 325.248 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0164 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.6251928 - 2.946147
Average (Standard dev.)-0.00031018077 (±0.05842946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 325.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42040_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_42040_half_map_1.map
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Half map: #1

Fileemd_42040_half_map_2.map
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Sample components

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Entire : 162bp NRCAM nucleosome in complex with scFv

EntireName: 162bp NRCAM nucleosome in complex with scFv
Components
  • Complex: 162bp NRCAM nucleosome in complex with scFv
    • 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
    • DNA: NRCAM DNA (162-MER)
    • DNA: NRCAM DNA (162-MER) complementary chain
    • Protein or peptide: scFv20

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Supramolecule #1: 162bp NRCAM nucleosome in complex with scFv

SupramoleculeName: 162bp NRCAM nucleosome in complex with scFv / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

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: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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-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: 14.165551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

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: 13.935239 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #7: scFv20

MacromoleculeName: scFv20 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.34542 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV ...String:
MKSSHHHHHH ENLYFQSNAM DIKMTQSPSS MHASLGERVT ITCKASQDIR SYLSWYQQKP WKSPKTLIYY ATSLADGVPS RFSGSGSGQ DFSLTINNLE SDDTATYYCL QHGESPYTFG SGTKLEIKRA GGGGSGGGGS GGGGSGGGGS MEVQLQQSGP E LVEPGTSV KMPCKASGYT FTSYTIQWVK QTPRQGLEWI GYIYPYNAGT KYNEKFKGKA TLTSDKSSST VYMELSSLTS ED SAVYYCA RKSSRLRSTL DYWGQGTSVT VSS

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Macromolecule #5: NRCAM DNA (162-MER)

MacromoleculeName: NRCAM DNA (162-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 49.86582 KDa
SequenceString: (DG)(DA)(DT)(DC)(DC)(DA)(DT)(DT)(DA)(DC) (DT)(DT)(DC)(DT)(DG)(DA)(DA)(DA)(DC)(DA) (DG)(DA)(DT)(DG)(DA)(DC)(DT)(DC)(DC) (DC)(DA)(DG)(DC)(DA)(DG)(DC)(DT)(DG)(DC) (DT) (DG)(DC)(DC)(DT)(DG)(DT) ...String:
(DG)(DA)(DT)(DC)(DC)(DA)(DT)(DT)(DA)(DC) (DT)(DT)(DC)(DT)(DG)(DA)(DA)(DA)(DC)(DA) (DG)(DA)(DT)(DG)(DA)(DC)(DT)(DC)(DC) (DC)(DA)(DG)(DC)(DA)(DG)(DC)(DT)(DG)(DC) (DT) (DG)(DC)(DC)(DT)(DG)(DT)(DG)(DG) (DC)(DC)(DC)(DA)(DC)(DA)(DG)(DG)(DG)(DC) (DT)(DT) (DC)(DC)(DT)(DG)(DC)(DC)(DC) (DT)(DG)(DC)(DA)(DT)(DG)(DA)(DC)(DA)(DG) (DC)(DT)(DG) (DC)(DA)(DC)(DA)(DT)(DC) (DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG) (DG)(DT)(DC)(DA) (DT)(DA)(DC)(DT)(DA) (DC)(DT)(DT)(DC)(DA)(DG)(DC)(DC)(DG)(DC) (DT)(DT)(DC)(DT)(DA) (DC)(DG)(DG)(DC) (DC)(DA)(DG)(DA)(DT)(DA)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DG)(DG) (DT)(DG)(DG) (DG)(DG)(DA)(DA)(DC)(DA)(DT)(DA)(DG)(DG) (DC)(DA)(DA)(DG)(DG)(DG)(DA) (DT)(DC)

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Macromolecule #6: NRCAM DNA (162-MER) complementary chain

MacromoleculeName: NRCAM DNA (162-MER) complementary chain / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 50.149953 KDa
SequenceString: (DG)(DA)(DT)(DC)(DC)(DC)(DT)(DT)(DG)(DC) (DC)(DT)(DA)(DT)(DG)(DT)(DT)(DC)(DC)(DC) (DC)(DA)(DC)(DC)(DC)(DA)(DC)(DT)(DT) (DT)(DT)(DG)(DT)(DA)(DT)(DC)(DT)(DG)(DG) (DC) (DC)(DG)(DT)(DA)(DG)(DA) ...String:
(DG)(DA)(DT)(DC)(DC)(DC)(DT)(DT)(DG)(DC) (DC)(DT)(DA)(DT)(DG)(DT)(DT)(DC)(DC)(DC) (DC)(DA)(DC)(DC)(DC)(DA)(DC)(DT)(DT) (DT)(DT)(DG)(DT)(DA)(DT)(DC)(DT)(DG)(DG) (DC) (DC)(DG)(DT)(DA)(DG)(DA)(DA)(DG) (DC)(DG)(DG)(DC)(DT)(DG)(DA)(DA)(DG)(DT) (DA)(DG) (DT)(DA)(DT)(DG)(DA)(DC)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DG) (DA)(DT)(DG) (DT)(DG)(DC)(DA)(DG)(DC) (DT)(DG)(DT)(DC)(DA)(DT)(DG)(DC)(DA)(DG) (DG)(DG)(DC)(DA) (DG)(DG)(DA)(DA)(DG) (DC)(DC)(DC)(DT)(DG)(DT)(DG)(DG)(DG)(DC) (DC)(DA)(DC)(DA)(DG) (DG)(DC)(DA)(DG) (DC)(DA)(DG)(DC)(DT)(DG)(DC)(DT)(DG)(DG) (DG)(DA)(DG)(DT)(DC)(DA) (DT)(DC)(DT) (DG)(DT)(DT)(DT)(DC)(DA)(DG)(DA)(DA)(DG) (DT)(DA)(DA)(DT)(DG)(DG)(DA) (DT)(DC)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 178787
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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