Biological Assembly 1  

 3D View: Structure | Electron Density

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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)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 202250.52 
• Atom Count: 11920 
• Residue Count: 1306 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

5XM1

The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4

• DOI: 10.2210/pdb5XM1/pdb

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli, Escherichia coli DH5[alpha]


• Deposited: 2017-05-12 Released: 2018-03-07 
• Deposition Author(s): Taguchi, H., Horikoshi, N., Kurumizaka, H.
• Funding Organization(s): Japan Society for the Promotion of Science; Ministry of Education, Culture, Sports, Science and Technology; the Japan Agency for Medical Research and Development 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.254 
• R-Value Work: 0.200 

Literature

The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4

Taguchi, H., Horikoshi, N., Kurumizaka, H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3mm7	A, E	139	Mus musculus	Mutation(s): 0  Gene Names: H3f3a, H3f3b (H3.3a, H3.3b)
Find proteins for P84244 (Mus musculus) Go to UniProtKB:  P84244

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F	106	Mus musculus	Mutation(s): 0  Gene Names: Hist1h4a, Hist1h4b, Hist1h4c, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist4h4 (H4-53, H4-12, Hist2h4)
Find proteins for P62806 (Mus musculus) Go to UniProtKB:  P62806

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A type 1-B	C, G	133	Mus musculus	Mutation(s): 0  Gene Names: Hist1h2ab
Find proteins for C0HKE1 (Mus musculus) Go to UniProtKB:  C0HKE1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B type 3-A	D, H	129	Mus musculus	Mutation(s): 0  Gene Names: Hist3h2ba
Find proteins for Q9D2U9 (Mus musculus) Go to UniProtKB:  Q9D2U9

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.254 
• R-Value Work: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 105.550	α = 90.00
b = 109.380	β = 90.00
c = 176.209	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-12 
• Released Date: 2018-03-07 
• Deposition Author(s): Taguchi, H., Horikoshi, N., Kurumizaka, H.

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

Revision History 

• Version 1.0: 2018-03-07
  Type: Initial release