Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 202448.47 
• Atom Count: 12081 
• Residue Count: 1306 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

5B2I

Human nucleosome containing CpG unmethylated DNA

• DOI: 10.2210/pdb5B2I/pdb
• NDB: 5B2I

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG', Escherichia coli HB101


• Deposited: 2016-01-16 Released: 2016-06-15 
• Deposition Author(s): Fujii, Y., Wakamori, M., Umehara, T., Yokoyama, S.
• Funding Organization(s): Japan Agency for Medical Research and development; Japan Science and Technology Agency; Ministry of Education, Culture, Sports, Science and Technology; Japan Society for the Promotion of Science London; Takeda Science Foundation 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.257 
• R-Value Work: 0.200 

Literature

Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation

Fujii, Y., Wakamori, M., Umehara, T., Yokoyama, S.

(2016) Febs Open Bio 6: 498-514

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 type 1-B/E	C, G	133	Homo sapiens	Gene Names: HIST1H2AB, HIST1H2AE (H2AFM, H2AFA)
Find proteins for P04908 (Homo sapiens) Go to Gene View: HIST1H2AB HIST1H2AE Go to UniProtKB:  P04908

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	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MN	E, I, J	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.257 
• R-Value Work: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 106.499	α = 90.00
b = 109.047	β = 90.00
c = 177.016	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-01-16 
• Released Date: 2016-06-15 
• Deposition Author(s): Fujii, Y., Wakamori, M., Umehara, T., Yokoyama, S.

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Funding Organization	Country	Grant Number
Japan Agency for Medical Research and development	Japan	the Platform Project for Supporting in Drug Discov
Japan Science and Technology Agency	Japan	PRESTO program
Ministry of Education, Culture, Sports, Science and Technology	Japan	Targeted Proteins Research Program (TPRP)
Japan Society for the Promotion of Science London	Japan	C24613007
Takeda Science Foundation	Japan	--

Revision History 

• Version 1.0: 2016-06-15
  Type: Initial release