9KQO | pdb_00009kqo

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

PDB DOI: https://doi.org/10.2210/pdb9KQO/pdb
EM Map EMD-62509: EMDB EMDataResource

Classification: NUCLEAR PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-11-26 Released: 2025-12-31
Deposition Author(s): Deng, Z.H., Ai, H.S., Liu, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

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

This is version 1.0 of the entry. See complete history.

Literature

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

Deng, Z.H., Tao, S.X., Du, Y.X., Li, Y.L., Liu, L., Ai, H.S.

To be published.

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

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase BRE1B	A	60	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75150
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B	75	Homo sapiens	Mutation(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
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J3QS39
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G	129	Homo sapiens	Mutation(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
PHAROS: P04908 GTEx: ENSG00000277075 ENSG00000278463
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04908
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-K	D, H	125	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60814
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D	Go to GlyGen: O60814-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	E, K	135	Homo sapiens	Mutation(s): 0 Gene Names: CALMAC_LOCUS17614
UniProt
Find proteins for A0A653DHJ5 (Callosobruchus maculatus) Explore A0A653DHJ5 Go to UniProtKB: A0A653DHJ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A653DHJ5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	F, L	102	Homo sapiens	Mutation(s): 0 Gene Names: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G... 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
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805 Go to UniProtKB: P62805
PHAROS: P62805 GTEx: ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62805
Sequence Annotations Expand
Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase BRE1A	M	60	Homo sapiens	Mutation(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
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5VTR2
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 A	N [auth R]	150	Homo sapiens	Mutation(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
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49459
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (147-MER)	I	147	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (147-MER)	J	147	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth M] SDF format, chain S [auth M] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth M] MOL2 format, chain S [auth M] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain R [auth M] mmCIF format, chain S [auth M]	O [auth A], P [auth A], R [auth M], S [auth M]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth M] Focus chain S [auth M] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth M] Focus chain S [auth M]

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:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	RELION	3.1
RECONSTRUCTION	RELION	3.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Deng, Z.H.

Ai, H.S.

Liu, L.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22137005, 92253302, 22227810 and T2488301, to L.L.; 32501108, to H.A.; 22207065, to Y.L.; 22277073, to M.P