Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 200.91 kDa 
• Atom Count: 11,893 
• Modelled Residue Count: 1,042 
• Deposited Residue Count: 1,302 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

 5B33

The crystal structure of the H2AZ nucleosome with H3.3.

• PDB DOI:  https://doi.org/10.2210/pdb5B33/pdb
• NDB: 5B33

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-08 Released: 2016-08-03 
• Deposition Author(s): Horikoshi, N., Taguchi, H., Arimura, Y., Kurumizaka, H.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan Society for the Promotion of Science, the Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.252 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Literature

Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A.

Horikoshi, N., Arimura, Y., Taguchi, H., Kurumizaka, H.

(2016) Open Biol 6

• PubMed: 27358293 
• DOI: https://doi.org/10.1098/rsob.160127
• Primary Citation of Related Structures:  
  5B31, 5B32, 5B33


• PubMed Abstract: 
  

H2A.Z is incorporated into nucleosomes located around transcription start sites and functions as an epigenetic regulator for the transcription of certain genes. During transcriptional regulation, the heterotypic H2A.Z/H2A nucleosome containing one each of H2A.Z and H2A is formed. However, previous homotypic H2A.Z nucleosome structures suggested that the L1 loop region of H2A.Z would sterically clash with the corresponding region of canonical H2A in the heterotypic nucleosome. To resolve this issue, we determined the crystal structures of heterotypic H2A.Z/H2A nucleosomes. In the H2A.Z/H2A nucleosome structure, the H2A.Z L1 loop structure was drastically altered without any structural changes of the canonical H2A L1 loop, thus avoiding the steric clash. Unexpectedly, the heterotypic H2A.Z/H2A nucleosome is more stable than the homotypic H2A.Z nucleosome. These data suggested that the flexible character of the H2A.Z L1 loop plays an essential role in forming the stable heterotypic H2A.Z/H2A nucleosome.

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Organizational Affiliation: 

Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	A, E	139	Homo sapiens	Mutation(s): 0  Gene Names: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B, H3-3A, H3-3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
PHAROS:  P84243

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	106	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.Z	C, G	131	Homo sapiens	Mutation(s): 0  Gene Names: H2AFZ, H2AZ, H2AZ1
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S5 (Homo sapiens) Explore P0C0S5  Go to UniProtKB:  P0C0S5
PHAROS:  P0C0S5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H	129	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BJ, H2BFR, H2BC11
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899
PHAROS:  P06899

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	I, J	146	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.252 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.799	α = 90
b = 109.872	β = 90
c = 181.931	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Horikoshi, N., Taguchi, H., Arimura, Y., Kurumizaka, H.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (MEXT)	Japan	25116002
Japan Society for the Promotion of Science	Japan	25250023
the Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Author supporting evidence, Data collection, Derived calculations