9KQO image
Deposition Date 2024-11-26
Release Date 2025-12-31
Last Version Date 2026-02-04
Entry Detail
PDB ID:
9KQO
Keywords:
Title:
cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Expression System(s):
Method Details:
Experimental Method:
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase B
Gene (Uniprot):RNF40
Chain IDs:A
Chain Length:60
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Polyubiquitin-B
Gene (Uniprot):UBB
Chain IDs:B
Chain Length:75
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B/E
Gene (Uniprot):H2AC4, H2AC8
Chain IDs:C, G
Chain Length:129
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-K
Gene (Uniprot):H2BC12
Chain IDs:D, H
Chain Length:125
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3
Gene (Uniprot):CALMAC_LOCUS17614
Chain IDs:E, K
Chain Length:135
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16
Chain IDs:F, L
Chain Length:102
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (147-MER)
Chain IDs:I
Chain Length:147
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (147-MER)
Chain IDs:J
Chain Length:147
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase B
Gene (Uniprot):RNF20
Chain IDs:M
Chain Length:60
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-conjugating enzyme
Gene (Uniprot):UBE2A
Chain IDs:N (auth: R)
Chain Length:150
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Allosteric activation of RNF20/RNF40-RAD6A-mediated H2BK120 monoubiquitylation by H2BS112 GlcNAcylation.
Nat.Chem.Biol. ? ? ? (2026)
PMID: 41495224 DOI: 10.1038/s41589-025-02109-6

Abstact

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.

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Primary Citation of related structures
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