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- EMDB-42093: Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome ... -

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Basic information

Entry
Database: EMDB / ID: EMD-42093
TitleCryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (Local Map 2)
Map data
Sample
  • Complex: 162bp NRCAM nucleosome in complex with Ascl1/E12a
    • Protein or peptide: Ascl1
    • Protein or peptide: E12a
Keywordsnucleosome / pioneer transcription factors / DNA binding proteins / transcription / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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: To Be Published
Title: Cryo-EM structure of NRCAM nucleosome aided by scFv
Authors: Zhou BR / Bai Y
History
DepositionSep 23, 2023-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42093.png

Downloads & links

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Map

FileDownload / File: emd_42093.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-5.007568 - 6.1225324
Average (Standard dev.)0.002756219 (±0.061878923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42093_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42093_half_map_2.map
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

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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: Homo sapiens (human)
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: Homo sapiens (human)
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

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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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 237174
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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