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- EMDB-72371: Human Oct4 bound to nucleosome reconstituted with human histones ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72371
TitleHuman Oct4 bound to nucleosome reconstituted with human histones and 182 bp human LIN28B sequence
Map dataElectron density map of Oct4 bound to LIN28B nucleosome
Sample
  • Complex: Human Oct4 bound to a Nucleosome with human histones and human LIN28 DNA sequence
    • Protein or peptide: OCT4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • DNA: LIN28B DNA
KeywordsTranscription factor / Oct4 / Nucleosome / Protein-DNA complex / Chromatin binding / Gene Regulation / Pioneer Factor / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsSinha KK / Halic M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nature / Year: 2023
Title: Histone modifications regulate pioneer transcription factor cooperativity.
Authors: Kalyan K Sinha / Silvija Bilokapic / Yongming Du / Deepshikha Malik / Mario Halic /
Abstract: Pioneer transcription factors have the ability to access DNA in compacted chromatin. Multiple transcription factors can bind together to a regulatory element in a cooperative way, and cooperation ...Pioneer transcription factors have the ability to access DNA in compacted chromatin. Multiple transcription factors can bind together to a regulatory element in a cooperative way, and cooperation between the pioneer transcription factors OCT4 (also known as POU5F1) and SOX2 is important for pluripotency and reprogramming. However, the molecular mechanisms by which pioneer transcription factors function and cooperate on chromatin remain unclear. Here we present cryo-electron microscopy structures of human OCT4 bound to a nucleosome containing human LIN28B or nMATN1 DNA sequences, both of which bear multiple binding sites for OCT4. Our structural and biochemistry data reveal that binding of OCT4 induces changes to the nucleosome structure, repositions the nucleosomal DNA and facilitates cooperative binding of additional OCT4 and of SOX2 to their internal binding sites. The flexible activation domain of OCT4 contacts the N-terminal tail of histone H4, altering its conformation and thus promoting chromatin decompaction. Moreover, the DNA-binding domain of OCT4 engages with the N-terminal tail of histone H3, and post-translational modifications at H3K27 modulate DNA positioning and affect transcription factor cooperativity. Thus, our findings suggest that the epigenetic landscape could regulate OCT4 activity to ensure proper cell programming.
History
DepositionAug 27, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72371.png

Downloads & links

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Map

FileDownload / File: emd_72371.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron density map of Oct4 bound to LIN28B nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 267.264 Å		1.04 Å/pix.
x 256 pix.
= 267.264 Å		1.04 Å/pix.
x 256 pix.
= 267.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.044 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.12635157 - 0.6415478
Average (Standard dev.)0.0034099913 (±0.03751415)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 267.264 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Oct4 bound to LIN28B nucleosome - half map A

Fileemd_72371_half_map_1.map
AnnotationOct4 bound to LIN28B nucleosome - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Oct4 bound to LIN28B nucleosome - half map B

Fileemd_72371_half_map_2.map
AnnotationOct4 bound to LIN28B nucleosome - half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Oct4 bound to a Nucleosome with human histones and human LI...

EntireName: Human Oct4 bound to a Nucleosome with human histones and human LIN28 DNA sequence
Components
  • Complex: Human Oct4 bound to a Nucleosome with human histones and human LIN28 DNA sequence
    • Protein or peptide: OCT4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • DNA: LIN28B DNA

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Supramolecule #1: Human Oct4 bound to a Nucleosome with human histones and human LI...

SupramoleculeName: Human Oct4 bound to a Nucleosome with human histones and human LIN28 DNA sequence
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: OCT4

MacromoleculeName: OCT4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSSHHHHHHS SGLVPRGSHM ASMTGGQQMG RDPNSMAGHL ASDFAFSPPP GGGGDGPGGP EPGWVDPRTW LSFQGPPGGP GIGPGVGPG SEVWGIPPCP PPYEFCGGMA YCGPQVGVGL VPQGGLETSQ PEGEAGVGVE SNSDGASPEP CTVTPGAVKL E KEKLEQNP ...String:
GSSHHHHHHS SGLVPRGSHM ASMTGGQQMG RDPNSMAGHL ASDFAFSPPP GGGGDGPGGP EPGWVDPRTW LSFQGPPGGP GIGPGVGPG SEVWGIPPCP PPYEFCGGMA YCGPQVGVGL VPQGGLETSQ PEGEAGVGVE SNSDGASPEP CTVTPGAVKL E KEKLEQNP EESQDIKALQ KELEQFAKLL KQKRITLGYT QADVGLTLGV LFGKVFSQTT ICRFEALQLS FKNMCKLRPL LQ KWVEEAD NNENLQEICK AETLVQARKR KRTSIENRVR GNLENLFLQC PKPTLQQISH IAQQLGLEKD VVRVWFCNRR QKG KRSSSD YAQREDFEAA GSPFSGGPVS FPLAPGPHFG TPGYGSPHFT ALYSSVPFPE GEAFPPVSVT TLGSPMHSN

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Macromolecule #2: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: S G R G K Q G G K A R A K A K T R S S R A G L Q F P V G R V H R L L R K G N Y A E R V G A G A P V Y L A A V L E Y L T A E I L E L A G N A A R D N K K T R I I P R H L Q L A I ...String:
S G R G K Q G G K A R A K A K T R S S R A G L Q F P V G R V H R L L R K G N Y A E R V G A G A P V Y L A A V L E Y L T A E I L E L A G N A A R D N K K T R I I P R H L Q L A I R N D E E L N K L L G K V T I A Q G G V L P N I Q A VL L P K K T E S H H K A K G K

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Macromolecule #3: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: P E P S K S A P A P K K G S K K A I T K A Q K K D G K K R K R S R K E S Y S I Y V Y K V L K Q V H P D T G I S S K A M G I M N S F V N D I F E R I A G E A S R L A H Y N K R S ...String:
P E P S K S A P A P K K G S K K A I T K A Q K K D G K K R K R S R K E S Y S I Y V Y K V L K Q V H P D T G I S S K A M G I M N S F V N D I F E R I A G E A S R L A H Y N K R S T I T S R E I Q T A V R L L L P G E L A K H A V S E GT K A V T K Y T S S K

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Macromolecule #4: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: A R T K Q T A R K S T G G K A P R K Q L A T K A A R K S A P A T G G V K K P H R Y R P G T V A L R E I R R Y Q K S T E L L I R K L P F Q R L V R E I A Q D F K T D L R F Q SS A ...String:
A R T K Q T A R K S T G G K A P R K Q L A T K A A R K S A P A T G G V K K P H R Y R P G T V A L R E I R R Y Q K S T E L L I R K L P F Q R L V R E I A Q D F K T D L R F Q SS A V M A L Q E A C E A Y L V G L F E D T N L C A I H A KR V T I M P K D I Q L A R R I R G E R A

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Macromolecule #5: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 5 / 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 #6: LIN28B DNA

MacromoleculeName: LIN28B DNA / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString: GCAT AAG T TA AGT GGT ATT AAC A TA TCC TCA GTG GTG A GT ATT AAC ATG GAA C TT ACT CCA ACA ATA C AG ATG CTG AAT AAA T GT AGT CTA AGT GAA G AA AGA AGG AAA GGT G GG AGC TGC CAT CAC T CA ...String:
GCAT AAG T TA AGT GGT ATT AAC A TA TCC TCA GTG GTG A GT ATT AAC ATG GAA C TT ACT CCA ACA ATA C AG ATG CTG AAT AAA T GT AGT CTA AGT GAA G AA AGA AGG AAA GGT G GG AGC TGC CAT CAC T CA GAA TTG TCC AGC A GG GAT TGT GCA AGC T TG TGA ATA AAG ACA C AT ACT TCA T

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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 / Component:
ConcentrationName
50.0 mMHEPES
1.0 mMDTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: NITROGEN / Chamber humidity: 95 % / Chamber temperature: 10 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 15080
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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