8VLR | pdb_00008vlr

Cryo-EM structure of native H2AK119bu nucleosome at 2.6

• PDB DOI: https://doi.org/10.2210/pdb8VLR/pdb
• EM Map EMD-43342: EMDB EMDataResource
• NAKB: 8VLR

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2024-01-12 Released: 2025-01-15 
• Deposition Author(s): Wang, Y., Zhang, K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Role of histone variants H2BC1 and H2AZ.2 in H2AK119ub nucleosome organization and Polycomb gene silencing

Shen, X.Y., Chen, C.X., Wang, Y., Zheng, W., Zheng, J.H., Jones, A.E., Zhu, B., Zhang, H., Lyons, C., Rijal, A., Moley, J.A., Cao, G.S., Liu, K., Winn, R., McGinty, R.K., Zhang, K., Wang, H.B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A5B3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 170.58 kDa 
• Atom Count: 11,657 
• Modeled Residue Count: 1,038 
• Deposited Residue Count: 1,038 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E	98	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	84	Homo sapiens	Mutation(s): 0
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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G	108	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
PHAROS:  P04908 GTEx:  ENSG00000277075 ENSG00000278463

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-A	D, H	93	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q96A08 (Homo sapiens) Explore Q96A08  Go to UniProtKB:  Q96A08
PHAROS:  Q96A08 GTEx:  ENSG00000146047

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (136-MER)	I [auth K]	136	Homo sapiens

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (136-MER)	J [auth L]	136	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Wang, Y., Zhang, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM130696
Department of Defense (DOD, United States)	United States	W81XWH-21-1-0714
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM142959

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release