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- EMDB-35383: RNF20-RNF40/hRad6A-Ub/nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-35383
TitleRNF20-RNF40/hRad6A-Ub/nucleosome complex
Map data3.12 angstrom map
Sample
  • Complex: RNF20-RNF40/hRAD6A-Ub in complex with nucleosome
    • Protein or peptide: x 8 types
    • DNA: x 2 types
  • Ligand: x 1 types
KeywordsRNF20 / RFN40 / RAD6 / nucleosome / H2BK120Ub / NUCLEAR PROTEIN
Function / homology
Function and homology information


histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / positive regulation of mitophagy / protein K11-linked ubiquitination / postreplication repair / RHOBTB1 GTPase cycle / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / protein K48-linked ubiquitination ...histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / positive regulation of mitophagy / protein K11-linked ubiquitination / postreplication repair / RHOBTB1 GTPase cycle / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / protein K48-linked ubiquitination / negative regulation of megakaryocyte differentiation / response to UV / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / negative regulation of cell migration / DNA methylation / Condensation of Prophase Chromosomes / epigenetic regulation of gene expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ubiquitin binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / mRNA 3'-UTR binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / 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 / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / RING-type E3 ubiquitin transferase / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / G2/M transition of mitotic cell cycle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / UCH proteinases / protein polyubiquitination / HCMV Early Events / ubiquitin-protein transferase activity / antimicrobial humoral immune response mediated by antimicrobial peptide / Antigen processing: Ubiquitination & Proteasome degradation / structural constituent of chromatin / ubiquitin protein ligase activity / p53 binding / antibacterial humoral response / E3 ubiquitin ligases ubiquitinate target proteins / late endosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / heterochromatin formation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / histone binding / defense response to Gram-negative bacterium / gene expression / Estrogen-dependent gene expression / killing of cells of another organism / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / chromosome, telomeric region
Similarity search - Function
E3 ubiquitin ligase Bre1 / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues ...E3 ubiquitin ligase Bre1 / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / 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 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H2B type 1-K / E3 ubiquitin-protein ligase BRE1B / Histone H2A type 1-B/E / Ubiquitin-conjugating enzyme E2 A / Histone H4 / Histone H3.1 / E3 ubiquitin-protein ligase BRE1A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsAi H / Deng Z / Sun M / Du Y / Pan M / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302, 22227810, 22277073, 92253302 China
CitationJournal: Mol Cell / Year: 2023
Title: Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A.
Authors: Zhiheng Deng / Huasong Ai / Maoshen Sun / Zebin Tong / Yunxiang Du / Qian Qu / Liying Zhang / Ziyu Xu / Shixian Tao / Qiang Shi / Jia-Bin Li / Man Pan / Lei Liu /
Abstract: Histone H2B monoubiquitylation plays essential roles in chromatin-based transcriptional processes. A RING-type E3 ligase (yeast Bre1 or human RNF20/RNF40) and an E2 ubiquitin-conjugating enzyme ...Histone H2B monoubiquitylation plays essential roles in chromatin-based transcriptional processes. A RING-type E3 ligase (yeast Bre1 or human RNF20/RNF40) and an E2 ubiquitin-conjugating enzyme (yeast Rad6 or human hRAD6A), together, precisely deposit ubiquitin on H2B K123 in yeast or K120 in humans. Here, we developed a chemical trapping strategy and successfully captured the transient structures of Bre1- or RNF20/RNF40-mediated ubiquitin transfer from Rad6 or hRAD6A to nucleosomal H2B. Our structures show that Bre1 and RNF40 directly bind nucleosomal DNA, exhibiting a conserved E3/E2/nucleosome interaction pattern from yeast to humans for H2B monoubiquitylation. We also find an uncanonical non-hydrophobic contact in the Bre1 RING-Rad6 interface, which positions Rad6 directly above the target H2B lysine residue. Our study provides mechanistic insights into the site-specific monoubiquitylation of H2B, reveals a critical role of nucleosomal DNA in mediating E3 ligase recognition, and provides a framework for understanding the cancer-driving mutations of RNF20/RNF40.
History
DepositionFeb 15, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35383.png

Downloads & links

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Map

FileDownload / File: emd_35383.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.12 angstrom map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.026784563 - 0.060762405
Average (Standard dev.)0.00020260223 (±0.001998662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3.87 angstrom map with intact E2

Fileemd_35383_additional_1.map
Annotation3.87 angstrom map with intact E2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3.02 angstrom map

Fileemd_35383_additional_2.map
Annotation3.02 angstrom map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35383_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35383_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : RNF20-RNF40/hRAD6A-Ub in complex with nucleosome

EntireName: RNF20-RNF40/hRAD6A-Ub in complex with nucleosome
Components
  • Complex: RNF20-RNF40/hRAD6A-Ub in complex with nucleosome
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2B type 1-K
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: E3 ubiquitin-protein ligase BRE1B
    • Protein or peptide: E3 ubiquitin-protein ligase BRE1A
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 A
  • Ligand: ZINC ION

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Supramolecule #1: RNF20-RNF40/hRAD6A-Ub in complex with nucleosome

SupramoleculeName: RNF20-RNF40/hRAD6A-Ub in complex with nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.936948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLG RVTIAQGGVL PNIQAVLLPK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #2: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.451957 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT CYTSA

UniProtKB: Histone H2B type 1-K

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Macromolecule #3: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.562577 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAC EAYLVGLFED TNLCAIHAKR VTIMPKDIQ LARRIRGER

UniProtKB: Histone H3.1

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.123692 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LRDNIQGITK PAIRRLARRG GVKRISGLIY EETRGVLKVF LENVIRDAVT YTEHAKRKTV TAMDVVYALK RQGRTLYGFG

UniProtKB: Histone H4

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Macromolecule #5: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.477994 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSA

UniProtKB: Histone H2B type 1-K

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Macromolecule #8: E3 ubiquitin-protein ligase BRE1B

MacromoleculeName: E3 ubiquitin-protein ligase BRE1B / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.120409 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString:
EYKARLTCPC CNTRKKDAVL TKCFHVFCFE CVRGRYEARQ RKCPKCNAAF GAHDFHRIYI

UniProtKB: E3 ubiquitin-protein ligase BRE1B

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Macromolecule #9: E3 ubiquitin-protein ligase BRE1A

MacromoleculeName: E3 ubiquitin-protein ligase BRE1A / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.14447 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString:
DYKARLTCPC CNMRKKDAVL TKCFHVFCFE CVKTRYDTRQ RKCPKCNAAF GANDFHRIYI

UniProtKB: E3 ubiquitin-protein ligase BRE1A

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Macromolecule #10: Ubiquitin-conjugating enzyme E2 A

MacromoleculeName: Ubiquitin-conjugating enzyme E2 A / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.114129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTPARRRLM RDFKRLQEDP PAGVSGAPSE NNIMVWNAVI FGPEGTPFED GTFKLTIEFT EEYPNKPPTV RFVSKMFHPN VYADGSICL DILQNRWSPT YDVSSILTSI QSLLDEPNPN SPANSQAAQL YQENKREYEK RVSAIVEQSW R

UniProtKB: Ubiquitin-conjugating enzyme E2 A

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Macromolecule #6: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.604047 KDa
SequenceString: (DA)(DC)(DA)(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) ...String:
(DA)(DC)(DA)(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)(DC)(DA)(DG)

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Macromolecule #7: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.145754 KDa
SequenceString: (DC)(DT)(DG)(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) ...String:
(DC)(DT)(DG)(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)(DT)(DG)(DT)

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 239429
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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