Biological Assembly 1  

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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: 200975.08 
• Atom Count: 11943 
• Residue Count: 1302 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

3WAA

The nucleosome containing human H2A.Z.2

• DOI: 10.2210/pdb3WAA/pdb
• NDB: NA2455

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2013-04-30 Released: 2013-12-18 
• Deposition Author(s): Horikoshi, N., Sato, K., Shimada, K., Arimura, Y., Osakabe, A., Tachiwana, H., Iwasaki, W., Kagawa, W., Harata, M., Kimura, H., Kurumizaka, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.2 Å
• R-Value Free: 0.271 
• R-Value Work: 0.217 

Literature

Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2

Horikoshi, N., Sato, K., Shimada, K., Arimura, Y., Osakabe, A., Tachiwana, H., Hayashi-Takanaka, Y., Iwasaki, W., Kagawa, W., Harata, M., Kimura, H., Kurumizaka, H.

(2013) Acta Crystallogr.,Sect.D 69: 2431-2439

• PubMed: 24311584 
• DOI: 10.1107/S090744491302252X
• Primary Citation of Related Structures:  
  3WA9


• PubMed Abstract: 
  

The histone H2A.Z variant is widely conserved among eukaryotes. Two isoforms, H2A.Z.1 and H2A.Z.2, have been identified in vertebrates and may have distinct functions in cell growth and gene expression. However, no structural differences between H2A.Z.1 and H2A.Z.2 have been reported. In the present study, the crystal structures of nucleosomes containing human H2A.Z.1 and H2A.Z.2 were determined. The structures of the L1 loop regions were found to clearly differ between H2A.Z.1 and H2A.Z.2, although their amino-acid sequences in this region are identical. This structural polymorphism may have been induced by a substitution that evolutionally occurred at the position of amino acid 38 and by the flexible nature of the L1 loops of H2A.Z.1 and H2A.Z.2. It was also found that in living cells nucleosomal H2A.Z.1 exchanges more rapidly than H2A.Z.2. A mutational analysis revealed that the amino-acid difference at position 38 is at least partially responsible for the distinctive dynamics of H2A.Z.1 and H2A.Z.2. These findings provide important new information for understanding the differences in the regulation and functions of H2A.Z.1 and H2A.Z.2 in cells.

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Organizational Affiliation: 

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.1	A, E	139	Homo sapiens	Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens) Go to Gene View: HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J Go to UniProtKB:  P68431

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F	106	Homo sapiens	Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens) Go to Gene View: HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4A HIST2H4B HIST4H4 Go to UniProtKB:  P62805

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A.V	C, G	131	Homo sapiens	Gene Names: H2AFV (H2AV)
Find proteins for Q71UI9 (Homo sapiens) Go to Gene View: H2AFV Go to UniProtKB:  Q71UI9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B type 1-J	D, H	129	Homo sapiens	Gene Names: HIST1H2BJ (H2BFR)
Find proteins for P06899 (Homo sapiens) Go to Gene View: HIST1H2BJ Go to UniProtKB:  P06899

Entity ID: 5
Molecule	Chains	Length	Organism
DNA (146-MER)	I,J	146	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.2 Å
• R-Value Free: 0.271 
• R-Value Work: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 105.359	α = 90.00
b = 109.842	β = 90.00
c = 182.992	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-30 
• Released Date: 2013-12-18 
• Deposition Author(s): Horikoshi, N., Sato, K., Shimada, K., Arimura, Y., Osakabe, A., Tachiwana, H., Iwasaki, W., Kagawa, W., Harata, M., Kimura, H., Kurumizaka, H.

Revision History 

• Version 1.0: 2013-12-18
  Type: Initial release