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- PDB-9kqo: cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112... -

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Basic information

Entry
Database: PDB / ID: 9kqo
Titlecryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome
Components
  • (DNA (147-MER)) x 2
  • (E3 ubiquitin-protein ligase ...) x 2
  • Histone H2A type 1-B/E
  • Histone H2B type 1-K
  • Histone H3
  • Histone H4
  • Polyubiquitin-B
  • Ubiquitin-conjugating enzyme E2 A
KeywordsNUCLEAR PROTEIN / RNF20 / RNF40 / H2BS112GlcNAc / O-GlcNAcylation / ubiquitination / H2BK120Ub
Function / homology
Function and homology information


histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / polytene chromosome / positive regulation of mitophagy / protein K11-linked ubiquitination / DNA damage tolerance / RHOBTB1 GTPase cycle / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin ligase complex ...histone H2B C-terminal K residue ubiquitin ligase activity / HULC complex / polytene chromosome / positive regulation of mitophagy / protein K11-linked ubiquitination / DNA damage tolerance / RHOBTB1 GTPase cycle / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / response to UV / protein K48-linked ubiquitination / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / 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 / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / negative regulation of cell migration / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / ubiquitin binding / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / innate immune response in mucosa / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / mRNA 3'-UTR binding / Negative Regulation of CDH1 Gene Transcription / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / RING-type E3 ubiquitin transferase / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / G2/M transition of mitotic cell cycle / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Metalloprotease DUBs / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / protein polyubiquitination / HCMV Early Events / p53 binding / ubiquitin-protein transferase activity / structural constituent of chromatin / ubiquitin protein ligase activity / UCH proteinases / late endosome / heterochromatin formation / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Antigen processing: Ubiquitination & Proteasome degradation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / histone binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / killing of cells of another organism / ubiquitin-dependent protein catabolic process / defense response to Gram-negative bacterium / proteasome-mediated ubiquitin-dependent protein catabolic process / mitochondrial outer membrane / transcription coactivator activity / chromosome, telomeric region / lysosome / Ub-specific processing proteases
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 H2A conserved site / Histone H2A signature. / Histone H2B 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Ubiquitin B / Histone H2B type 1-K / E3 ubiquitin-protein ligase BRE1B / Histone H2A type 1-B/E / Ubiquitin-conjugating enzyme E2 A / Histone H4 / E3 ubiquitin-protein ligase BRE1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsDeng, Z.H. / Ai, H.S. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302, 22227810 and T2488301, to L.L.; 32501108, to H.A.; 22207065, to Y.L.; 22277073, to M.P China
CitationJournal: Nat Chem Biol / Year: 2026
Title: Allosteric activation of RNF20/RNF40-RAD6A-mediated H2BK120 monoubiquitylation by H2BS112 GlcNAcylation.
Authors: Zhiheng Deng / Shixian Tao / Yunxiang Du / Yulei Li / Liying Zhang / Qiang Shi / Xiaoru Du / Maoshen Sun / Zebin Tong / Man Pan / Lei Liu / Huasong Ai /
Abstract: The activation of H2B K120 monoubiquitylation (H2BK120ub) by H2B S112 GlcNAcylation (H2BS112GlcNAc) has an important role in regulating transcriptional activation, yet its mechanism remains unclear. ...The activation of H2B K120 monoubiquitylation (H2BK120ub) by H2B S112 GlcNAcylation (H2BS112GlcNAc) has an important role in regulating transcriptional activation, yet its mechanism remains unclear. Here we chemically synthesized H2BS112GlcNAc-modified nucleosomes and quantitatively evaluated how H2BS112GlcNAc stimulates ubiquitylation by RNF20/RNF40-RAD6A E3-E2 enzymes. Cryo-electron microscopy determination of a chemically trapped RNF20/RNF40-RAD6A-Ub-H2BS112GlcNAc nucleosome complex revealed that the H2BS112GlcNAc moiety interacts with the E2 enzyme RAD6A but not the E3 ligase RNF20/RNF40. Mutagenesis and kinetics analyses demonstrated that H2BS112GlcNAc allosterically stimulates ubiquitin transfer from the RAD6A~Ub thioester to H2B K120 by enhancing the nucleophilicity of H2B K120. Structure‒activity relationship analysis further identified the essential roles of the C2 N-acetyl group and the β-configuration of C1 on the H2BS112GlcNAc moiety. These findings provide the structural evidence of histone posttranslational modification crosstalk involving O-GlcNAcylation and reveal how O-GlcNAcylation can allosterically stimulate enzyme activity through substrate modification.
History
DepositionNov 26, 2024Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase BRE1B
B: Polyubiquitin-B
C: Histone H2A type 1-B/E
D: Histone H2B type 1-K
E: Histone H3
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-K
I: DNA (147-MER)
J: DNA (147-MER)
K: Histone H3
L: Histone H4
M: E3 ubiquitin-protein ligase BRE1A
R: Ubiquitin-conjugating enzyme E2 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,80219
Polymers239,31914
Non-polymers4835
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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E3 ubiquitin-protein ligase ... , 2 types, 2 molecules AM

#1: Protein E3 ubiquitin-protein ligase BRE1B / BRE1-B / 95 kDa retinoblastoma-associated protein / RBP95 / RING finger protein 40 / RING-type E3 ...BRE1-B / 95 kDa retinoblastoma-associated protein / RBP95 / RING finger protein 40 / RING-type E3 ubiquitin transferase BRE1B


Mass: 7120.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF40, BRE1B, KIAA0661 / Production host: Escherichia coli (E. coli)
References: UniProt: O75150, RING-type E3 ubiquitin transferase
#9: Protein E3 ubiquitin-protein ligase BRE1A / BRE1-A / hBRE1 / RING finger protein 20 / RING-type E3 ubiquitin transferase BRE1A


Mass: 7144.470 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF20, BRE1A / Production host: Escherichia coli (E. coli)
References: UniProt: Q5VTR2, RING-type E3 ubiquitin transferase

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Protein , 6 types, 10 molecules BCGDHEKFLR

#2: Protein Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14034.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein Histone H2B type 1-K / H2B K / HIRA-interacting protein 1


Mass: 13763.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC12, H2BFT, HIRIP1, HIST1H2BK / Production host: Escherichia coli (E. coli) / References: UniProt: O60814
#5: Protein Histone H3


Mass: 15273.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALMAC_LOCUS17614 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A653DHJ5
#6: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#10: Protein Ubiquitin-conjugating enzyme E2 A / E2 ubiquitin-conjugating enzyme A / RAD6 homolog A / HR6A / hHR6A / Ubiquitin carrier protein A / ...E2 ubiquitin-conjugating enzyme A / RAD6 homolog A / HR6A / hHR6A / Ubiquitin carrier protein A / Ubiquitin-protein ligase A


Mass: 17114.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2A, RAD6A / Production host: Escherichia coli (E. coli)
References: UniProt: P49459, E2 ubiquitin-conjugating enzyme

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DNA chain , 2 types, 2 molecules IJ

#7: DNA chain DNA (147-MER)


Mass: 45604.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#8: DNA chain DNA (147-MER)


Mass: 45145.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers / Sugars , 2 types, 5 molecules

#11: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#12: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RNF20/RNF40-RAD6A-Ub bound to H2BS112GlcNAc nucleosome
Type: COMPLEX / Entity ID: #1-#10 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 18000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing-ID
1RELION3.1particle selection1
2PHENIX1.21.1_5286model refinement
13RELION3.13D reconstruction1
14RELION3.1particle selection2
19RELION3.13D reconstruction2
Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11NONE
22NONE
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.48FSC 0.143 CUT-OFF11960219KQOPOINT
23.48FSC 0.143 CUT-OFF11960219KQOPOINT
33.48FSC 0.143 CUT-OFF11960219KQOPOINT
43.48FSC 0.143 CUT-OFF11960219KQOPOINT
53.48FSC 0.143 CUT-OFF11960219KQOPOINT
63.48FSC 0.143 CUT-OFF11960219KQOPOINT
73.48FSC 0.143 CUT-OFF11960219KQOPOINT
83.48FSC 0.143 CUT-OFF11960219KQOPOINT
93.48FSC 0.143 CUT-OFF11960219KQOPOINT
103.48FSC 0.143 CUT-OFF11960219KQOPOINT
113.48FSC 0.143 CUT-OFF11960219KQOPOINT
123.48FSC 0.143 CUT-OFF11960219KQOPOINT
133.48FSC 0.143 CUT-OFF11960219KQOPOINT
143.48FSC 0.143 CUT-OFF11960219KQOPOINT
153.48FSC 0.143 CUT-OFF11960219KQOPOINT
163.48FSC 0.143 CUT-OFF11960219KQOPOINT
173.48FSC 0.143 CUT-OFF11960229KQOPOINT
183.48FSC 0.143 CUT-OFF11960229KQOPOINT
193.48FSC 0.143 CUT-OFF11960229KQOPOINT
203.48FSC 0.143 CUT-OFF11960229KQOPOINT
213.48FSC 0.143 CUT-OFF11960229KQOPOINT
223.48FSC 0.143 CUT-OFF11960229KQOPOINT
233.48FSC 0.143 CUT-OFF11960229KQOPOINT
243.48FSC 0.143 CUT-OFF11960229KQOPOINT
253.48FSC 0.143 CUT-OFF11960229KQOPOINT
263.48FSC 0.143 CUT-OFF11960229KQOPOINT
273.48FSC 0.143 CUT-OFF11960229KQOPOINT
283.48FSC 0.143 CUT-OFF11960229KQOPOINT
293.48FSC 0.143 CUT-OFF11960229KQOPOINT
303.48FSC 0.143 CUT-OFF11960229KQOPOINT
313.48FSC 0.143 CUT-OFF11960229KQOPOINT
323.48FSC 0.143 CUT-OFF11960229KQOPOINT
RefinementHighest resolution: 3.48 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415564
ELECTRON MICROSCOPYf_angle_d0.60922295
ELECTRON MICROSCOPYf_dihedral_angle_d28.7384455
ELECTRON MICROSCOPYf_chiral_restr0.0422533
ELECTRON MICROSCOPYf_plane_restr0.0061815

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