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- EMDB-62757: hDEK-nucleosome complex (conformation 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-62757
TitlehDEK-nucleosome complex (conformation 1)
Map data
Sample
  • Complex: hDEK-NCP complex conformation 1
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: 601 DNA_R (189-MER)
    • DNA: 601 DNA (189-MER)
    • Protein or peptide: Protein DEK
  • Ligand: UNKNOWN ATOM OR ION
Keywordsnucleosome complex / GENE REGULATION
Function / homology
Function and homology information


regulation of double-strand break repair via nonhomologous end joining / contractile muscle fiber / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / B-WICH complex / pericentric heterochromatin formation / inner kinetochore / regulation of double-strand break repair ...regulation of double-strand break repair via nonhomologous end joining / contractile muscle fiber / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / B-WICH complex / pericentric heterochromatin formation / inner kinetochore / regulation of double-strand break repair / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / positive regulation of transcription by RNA polymerase III / nucleus organization / spermatid development / positive regulation of transcription by RNA polymerase I / single fertilization / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / RNA polymerase II core promoter sequence-specific DNA binding / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / viral genome replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / heterochromatin formation / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / male gonad development / nucleosome assembly / osteoblast differentiation / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / defense response to Gram-negative bacterium / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / histone binding / transcription by RNA polymerase II / chromosome, telomeric region / cell population proliferation
Similarity search - Function
Protein DEK / DEK C terminal domain / DEK, C-terminal / DEK C-terminal (DEK-C) domain profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / : / Histone H2B signature. / Histone H2B ...Protein DEK / DEK C terminal domain / DEK, C-terminal / DEK C-terminal (DEK-C) domain profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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 / Histone-fold
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Protein DEK / Histone H4 / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsLiu Y / Wang C / Huang H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171206 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: DEK-nucleosome structure shows DEK modulates H3K27me3 and stem cell fate.
Authors: Yunfan Shen / Yanhong Liu / Maochao Guo / Song Mao / Rui Chen / Mengran Wang / Zhengbo Li / Yue Li / Wan Chen / Fang Chen / Baixing Wu / Chongyuan Wang / Wei Chen / Huanhuan Cui / Kai Yuan / Hongda Huang /
Abstract: DEK is a highly conserved chromatin-associated oncoprotein that has important roles in regulating chromatin dynamics and stem cell fate. Dysregulation of DEK is associated with stem cell dysfunction ...DEK is a highly conserved chromatin-associated oncoprotein that has important roles in regulating chromatin dynamics and stem cell fate. Dysregulation of DEK is associated with stem cell dysfunction and cancers, including acute myeloid leukemia. Despite its importance in chromatin regulation, the structural mechanisms underlying DEK's interaction with chromatin and its influence on gene regulation remain poorly understood. Here we combined cryogenic electron microscopy (cryo-EM), biochemical and cellular approaches to investigate the molecular mechanisms and functional importance of DEK's interaction with chromatin. Our cryo-EM structures reveal the structural basis of the DEK-nucleosome interaction. Biochemical and cellular results demonstrate that this interaction is crucial for DEK deposition onto chromatin. Furthermore, our results reveal that DEK safeguards mouse embryonic stem cells from acquiring primitive endoderm fates by modulating the repressive histone mark H3K27me3. Together, our study provides crucial molecular insights into the structure and function of DEK, establishing a framework for understanding its roles in chromatin biology and cell fate determination.
History
DepositionDec 16, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62757.png

Downloads & links

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Map

FileDownload / File: emd_62757.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 303.12 Å		0.84 Å/pix.
x 360 pix.
= 303.12 Å		0.84 Å/pix.
x 360 pix.
= 303.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.293
Minimum - Maximum-2.0237198 - 5.287692
Average (Standard dev.)0.0027348269 (±0.11642531)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 303.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62757_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62757_half_map_2.map
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Sample components

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Entire : hDEK-NCP complex conformation 1

EntireName: hDEK-NCP complex conformation 1
Components
  • Complex: hDEK-NCP complex conformation 1
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: 601 DNA_R (189-MER)
    • DNA: 601 DNA (189-MER)
    • Protein or peptide: Protein DEK
  • Ligand: UNKNOWN ATOM OR ION

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Supramolecule #1: hDEK-NCP complex conformation 1

SupramoleculeName: hDEK-NCP complex conformation 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.229787 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP STGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSAAI GALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.3

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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: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

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: 12.925096 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK

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: 13.804045 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #7: Protein DEK

MacromoleculeName: Protein DEK / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.759449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSASAPAAEG EGTPTQPASE KEPEMPGPRE ESEEEEDEDD EEEEEEEKEK SLIVEGKREK KKVERLTMQV SSLQREPFTI AQGKGQKLC EIERIHFFLS KKKTDELRNL HKLLYNRPGT VSSLKKNVGQ FSGFPFEKGS VQYKKKEEML KKFRNAMLKS I CEVLDLER ...String:
MSASAPAAEG EGTPTQPASE KEPEMPGPRE ESEEEEDEDD EEEEEEEKEK SLIVEGKREK KKVERLTMQV SSLQREPFTI AQGKGQKLC EIERIHFFLS KKKTDELRNL HKLLYNRPGT VSSLKKNVGQ FSGFPFEKGS VQYKKKEEML KKFRNAMLKS I CEVLDLER SGVNSELVKR ILNFLMHPKP SGKPLPKSKK TCSKGSKKER NSSGMARKAK RTKCPEILSD ESSSDEDEKK NK EESSDDE DKESEEEPPK KTAKREKPKQ KATSKSKKSV KSANVKKADS STTKKNQNSS KKESESEDSS DDEPLIKKLK KPP TDEELK ETIKKLLASA NLEEVTMKQI CKKVYENYPT YDLTERKDFI KTTVKELIS

UniProtKB: Protein DEK

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Macromolecule #5: 601 DNA_R (189-MER)

MacromoleculeName: 601 DNA_R (189-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.551277 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DC)(DG)(DA)(DC)(DA) (DC)(DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG) (DA)(DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG) (DA) (DC)(DA)(DC)(DG)(DT)(DG) ...String:
(DA)(DT)(DC)(DA)(DG)(DC)(DG)(DA)(DC)(DA) (DC)(DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG) (DA)(DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG) (DA) (DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC) (DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG) (DG)(DG) (DA)(DG)(DT)(DA)(DA)(DT)(DC) (DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG) (DT)(DT)(DA) (DA)(DA)(DA)(DC)(DG)(DC) (DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC) (DG)(DC)(DG)(DT) (DA)(DC)(DG)(DT)(DG) (DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG) (DG)(DT)(DG)(DC)(DT) (DA)(DG)(DA)(DG) (DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA) (DC)(DC)(DA)(DA)(DT)(DT) (DG)(DA)(DG) (DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC) (DA)(DC)(DC)(DG)(DG)(DG)(DA) (DT)(DT) (DC)(DT)(DC)(DG)(DA)(DT)(DG)(DG)(DC)(DA) (DT)(DC)(DC)(DG)(DG)(DC)(DA)(DT) (DC) (DA)(DC)(DC)(DC)(DG)(DG)(DA)(DT)

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Macromolecule #6: 601 DNA (189-MER)

MacromoleculeName: 601 DNA (189-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.154988 KDa
SequenceString: (DA)(DT)(DC)(DC)(DG)(DG)(DG)(DT)(DG)(DA) (DT)(DG)(DC)(DC)(DG)(DG)(DA)(DT)(DG)(DC) (DC)(DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA) (DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG) (DA)(DG)(DG)(DC)(DC)(DG) ...String:
(DA)(DT)(DC)(DC)(DG)(DG)(DG)(DT)(DG)(DA) (DT)(DG)(DC)(DC)(DG)(DG)(DA)(DT)(DG)(DC) (DC)(DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA) (DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT) (DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG) (DT)(DA) (DG)(DA)(DC)(DA)(DG)(DC)(DT) (DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC) (DT)(DT)(DA) (DA)(DA)(DC)(DG)(DC)(DA) (DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT) (DG)(DT)(DC)(DC) (DC)(DC)(DC)(DG)(DC) (DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG) (DC)(DC)(DA)(DA)(DG) (DG)(DG)(DG)(DA) (DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA) (DG)(DT)(DC)(DT)(DC)(DC) (DA)(DG)(DG) (DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG) (DA)(DT)(DA)(DT)(DA)(DT)(DA) (DC)(DA) (DT)(DC)(DC)(DG)(DA)(DT)(DT)(DC)(DC)(DA) (DG)(DT)(DG)(DC)(DC)(DG)(DG)(DT) (DG) (DT)(DC)(DG)(DC)(DT)(DG)(DA)(DT)

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Macromolecule #8: UNKNOWN ATOM OR ION

MacromoleculeName: UNKNOWN ATOM OR ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: UNX

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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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180577
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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