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 9KQO | pdb_00009kqo

cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9KQO

This is version 1.2 of the entry. See complete history. 

Literature

Allosteric activation of RNF20/RNF40-RAD6A-mediated H2BK120 monoubiquitylation by H2BS112 GlcNAcylation.

Deng, Z., Tao, S., Du, Y., Li, Y., Zhang, L., Shi, Q., Du, X., Sun, M., Tong, Z., Pan, M., Liu, L., Ai, H.

(2026) Nat Chem Biol 22: 740-750

  • DOI: https://doi.org/10.1038/s41589-025-02109-6
  • Primary Citation Related Structures: 
    9KQO

  • PubMed 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. 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.


  • Organizational Affiliation: 
    • School of Pharmaceutical Sciences, Institute of Translational Medicine, Shanghai Key Laboratory for Antibody-Drug Conjugates with Innovative Target, Shanghai Frontiers Science Center of Drug Target Identification and Delivery, Shanghai Jiao Tong University, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 239.8 kDa 
  • Atom Count: 14,687 
  • Modeled Residue Count: 1,399 
  • Deposited Residue Count: 1,621 
  • Unique protein chains: 8
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase BRE1B60Homo sapiensMutation(s): 0 
Gene Names: RNF40, BRE1B, KIAA0661
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for O75150 (Homo sapiens)
Explore O75150 
Go to UniProtKB:  O75150
PHAROS:  O75150
GTEx:  ENSG00000103549 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75150
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Polyubiquitin-B75Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for J3QS39 (Homo sapiens)
Explore J3QS39 
Go to UniProtKB:  J3QS39
GTEx:  ENSG00000170315 
Entity Groups
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UniProt GroupJ3QS39
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
129Homo sapiensMutation(s): 0 
Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
Entity Groups
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UniProt GroupP04908
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B type 1-K
D, H
125Homo sapiensMutation(s): 0 
Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens)
Explore O60814 
Go to UniProtKB:  O60814
PHAROS:  O60814
GTEx:  ENSG00000197903 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60814
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O60814-1
Sequence Annotations
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3
E, K
135Homo sapiensMutation(s): 0 
Gene Names: CALMAC_LOCUS17614
UniProt
Find proteins for A0A653DHJ5 (Callosobruchus maculatus)
Explore A0A653DHJ5 
Go to UniProtKB:  A0A653DHJ5
Entity Groups
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UniProt GroupA0A653DHJ5
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4
F, L
102Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
Entity Groups
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UniProt GroupP62805
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase BRE1A60Homo sapiensMutation(s): 0 
Gene Names: RNF20, BRE1A
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VTR2 (Homo sapiens)
Explore Q5VTR2 
Go to UniProtKB:  Q5VTR2
PHAROS:  Q5VTR2
GTEx:  ENSG00000155827 
Entity Groups
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UniProt GroupQ5VTR2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 AN [auth R]150Homo sapiensMutation(s): 0 
Gene Names: UBE2A, RAD6A
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P49459 (Homo sapiens)
Explore P49459 
Go to UniProtKB:  P49459
PHAROS:  P49459
GTEx:  ENSG00000077721 
Entity Groups
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UniProt GroupP49459
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (147-MER)147Homo sapiens
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (147-MER)147Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Resolution: 3.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONRELION3.1
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22137005, 92253302, 22227810 and T2488301, to L.L.; 32501108, to H.A.; 22207065, to Y.L.; 22277073, to M.P

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-31
    Type: Initial release
  • Version 1.1: 2026-02-04
    Changes: Data collection, Database references
  • Version 1.2: 2026-05-13
    Changes: Data collection, Database references