9B3P

The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome

• PDB DOI: https://doi.org/10.2210/pdb9B3P/pdb
• NAKB: 9B3P
• EM Map EMD-44148: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Homo sapiens, Xenopus laevis, Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-19 Released: 2024-06-12 
• Deposition Author(s): Tan, D., Sokolova, V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and Biochemical Characterization of the Nucleosome Containing Variants H3.3 and H2A.Z

Jung, H., Sokolova, V., Lee, G., Stevens, V.R., Tan, D.

(2024) Epigenomes 

• DOI: https://doi.org/10.3390/epigenomes8020021

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 - A7B1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 205.48 kDa 
• Atom Count: 11,067 
• Modelled Residue Count: 994 
• Deposited Residue Count: 1,300 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	A, E	136	Homo sapiens	Mutation(s): 0  Gene Names: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
PHAROS:  P84243 GTEx:  ENSG00000132475 ENSG00000163041

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.Z	C, G	128	Mus musculus	Mutation(s): 0  Gene Names: H2az1, H2afz, H2az
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S6 (Mus musculus) Explore P0C0S6  Go to UniProtKB:  P0C0S6
IMPC:  MGI:1888388

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H	126	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (128-MER)	I	147	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (128-MER)	J	167	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	PHENIX	1.15.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Tan, D., Sokolova, V.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM133611
National Science Foundation (NSF, United States)	United States	1942049

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release