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- EMDB-75506: Cryo-EM map of Ascl1-E12a in complex with NRCAM nucleosome withou... -

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Basic information

Entry
Database: EMDB / ID: EMD-75506
TitleCryo-EM map of Ascl1-E12a in complex with NRCAM nucleosome without scFv
Map datacryo-EM of Ascl1-E12a in complex with 162bp NRCAM nucleosome
Sample
  • Complex: 162bp NRCAM nucleosome in complex with Ascl1/E12a
    • Protein or peptide: Ascl1
    • Protein or peptide: E12a
    • Protein or peptide: H2A
    • Protein or peptide: H2B
    • Protein or peptide: H3
    • Protein or peptide: H4
    • DNA: 162 bp NRCAM DNA
    • DNA: 162 bp NRCAM DNA complementary strand
Keywordsnucleosome / pioneer transcription factors / DNA binding proteins / transcription / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.33 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
DepositionFeb 11, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75506.png

Downloads & links

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Map

FileDownload / File: emd_75506.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM of Ascl1-E12a in complex with 162bp NRCAM nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.24 Å/pix.
x 128 pix.
= 286.72 Å		2.24 Å/pix.
x 128 pix.
= 286.72 Å		2.24 Å/pix.
x 128 pix.
= 286.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.282
Minimum - Maximum-0.4155997 - 1.7130723
Average (Standard dev.)0.0036046312 (±0.085619345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 286.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map2

Fileemd_75506_half_map_1.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map1

Fileemd_75506_half_map_2.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 162bp NRCAM nucleosome in complex with Ascl1/E12a

EntireName: 162bp NRCAM nucleosome in complex with Ascl1/E12a
Components
  • Complex: 162bp NRCAM nucleosome in complex with Ascl1/E12a
    • Protein or peptide: Ascl1
    • Protein or peptide: E12a
    • Protein or peptide: H2A
    • Protein or peptide: H2B
    • Protein or peptide: H3
    • Protein or peptide: H4
    • DNA: 162 bp NRCAM DNA
    • DNA: 162 bp NRCAM DNA complementary strand

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Supramolecule #1: 162bp NRCAM nucleosome in complex with Ascl1/E12a

SupramoleculeName: 162bp NRCAM nucleosome in complex with Ascl1/E12a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ascl1

MacromoleculeName: Ascl1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MESSGKMESG AGQQPQPPQP FLPPAACFFA TAAAAAAAAA AAAQSAQQQQ PQAPPQQAPQ LSPVADSQP SGGGHKSAAK QVKRQRSSSP ELMRCKRRLN FSGFGYSLPQ QQPAAVARRN E RERNRVKL VNLGFATLRE HVPNGAANKK MSKVETLRSA VEYIRALQQL ...String:
MESSGKMESG AGQQPQPPQP FLPPAACFFA TAAAAAAAAA AAAQSAQQQQ PQAPPQQAPQ LSPVADSQP SGGGHKSAAK QVKRQRSSSP ELMRCKRRLN FSGFGYSLPQ QQPAAVARRN E RERNRVKL VNLGFATLRE HVPNGAANKK MSKVETLRSA VEYIRALQQL LDEHDAVSAA FQ AGVLSPT ISPNYSNDLN SMAGSPVSSY SSDEGSYDPL SPEEQELLDF TNWF

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Macromolecule #2: E12a

MacromoleculeName: E12a / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MMNQSQRMAP VGSDKELSDL LDFSMMFPLP VANGKSRPAS LGGTQFAGSG LEDRPSSGSW GSSDQNSSS FDPSRTYSEG AHFSDSHSSL PPSTFLGAGL GGKGSERNAY ATFGRDTSVG T LSQAGFLP GELSLSSPGP LSPSGIKSSS QYYPSFPSNP RRRAADGGLD ...String:
MMNQSQRMAP VGSDKELSDL LDFSMMFPLP VANGKSRPAS LGGTQFAGSG LEDRPSSGSW GSSDQNSSS FDPSRTYSEG AHFSDSHSSL PPSTFLGAGL GGKGSERNAY ATFGRDTSVG T LSQAGFLP GELSLSSPGP LSPSGIKSSS QYYPSFPSNP RRRAADGGLD TQPKKVRKVP PG LPSSVYP PSSGDSYSRD AAAYPSAKTP SSAYPSPFYV ADGSLHPSAE LWSTPSQVGF GPM LGDGSS PLPLAPGSSS VGSGTFGGLQ QQDRMGYQLH GSEVNGSLPA VSSFSAAPGT YSGT SGHTP PVSGAAAESL LGTRGTTASS SGDALGKALA SIYSPDHSSN NFSPSPSTPV GSPQG LPGT SQWPRAGAPS ALSPNYDAGL HGLSKMEDRL DEAIHVLRSH AVGTASDLHG LLPGHG ALT TSFTGPMSLG GRHAGLVGGS HPEEGLTSGA SLLHNHASLP SQPSSLPDLS QRPPDSY SG LGRAGTTAGA SEIKREEKED EEIASVADAE EDKKDLKVPR TRTSPDEDED DLLPPEQK A EREKERRVAN NARERLRVRD INEAFKELGR MCQLHLSSEK PQTKLLILHQ AVAVILSLE QQVRERNLNP KAACLKRREE EKVSGVVGDP QLALSAAHPG LGEAHNPAGH L AGVLSPTI SPNYSNDLNS MAGSPVSSYS SDEGSYDPLS PEEQELLDFT NWF

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Macromolecule #3: H2A

MacromoleculeName: H2A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

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Macromolecule #4: H2B

MacromoleculeName: H2B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

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Macromolecule #5: H3

MacromoleculeName: H3 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

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Macromolecule #6: H4

MacromoleculeName: H4 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

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Macromolecule #7: 162 bp NRCAM DNA

MacromoleculeName: 162 bp NRCAM DNA / type: dna / ID: 7 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
SequenceString:
GATCCATTAC TTCTGAAACA GATGACTCCC AGCAGCTGCT GCCTGTGGCC CACAGGGCTT CCTGCCCTGC ATGACAGCTG CACATCACAT CCTGTGGTCA TACTACTTCA GCCGCTTCTA CGGCCAGATA CAAAAGTGGG TGGGGAACAT AGGCAAGGGA TC

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Macromolecule #8: 162 bp NRCAM DNA complementary strand

MacromoleculeName: 162 bp NRCAM DNA complementary strand / type: dna / ID: 8 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
SequenceString:
GATCCCTTGC CTATGTTCCC CACCCACTTT TGTATCTGGC CGTAGAAGCG GCTGAAGTAG TATGACCACA GGATGTGATG TGCAGCTGTC ATGCAGGGCA GGAAGCCCTG TGGGCCACAG GCAGCAGCTG CTGGGAGTCA TCTGTTTCAG AAGTAATGGA TC

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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 K3 (6k 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: 7.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 11736
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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