8V25

H2BK120ub-modified nucleosome ubiquitin position 1

• PDB DOI: https://doi.org/10.2210/pdb8V25/pdb
• EM Map EMD-42898: EMDB EMDataResource
• NAKB: 8V25

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-11-21 Released: 2024-08-28 
• Deposition Author(s): Hicks, C.W., Wolberger, C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.32 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch

Hicks, C.W., Rahman, S., Gloor, S.L., Fields, J.K., Husby, N.L., Vaidya, A., Maier, K.E., Morgan, M., Keogh, M.C., Wolberger, C.

(2024) Nucleic Acids Res 

• DOI: https://doi.org/10.1093/nar/gkae698

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B1C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 208.92 kDa 
• Atom Count: 12,689 
• Modelled Residue Count: 1,139 
• Deposited Residue Count: 1,358 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	136	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	Xenopus laevis	Mutation(s): 0  Gene Names: LOC121398084
UniProt
Find proteins for A0A8J1LTD2 (Xenopus laevis) Explore A0A8J1LTD2  Go to UniProtKB:  A0A8J1LTD2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	130	Xenopus laevis	Mutation(s): 0  Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8  Go to UniProtKB:  Q6AZJ8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H	123	Xenopus laevis	Mutation(s): 2
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	K	80	Homo sapiens	Mutation(s): 1  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Entity ID: 5
Molecule	Chains	Length	Organism	Image
601 DNA (147-MER)	I	147	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
601 DNA (147-MER)	J	147	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.32 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Hicks, C.W., Wolberger, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R35GM130393
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	F31CA261154

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release
  
• Version 1.1: 2024-09-11
  Changes: Data collection, Database references