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)

Macromolecule Content

• Total Structure Weight: 201614.30 
• Atom Count: 11974 
• Residue Count: 1302 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

4YM5

Crystal structure of the human nucleosome containing 6-4PP (inside)

• DOI: 10.2210/pdb4YM5/pdb
• NDB: 4YM5

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli


• Deposited: 2015-03-06 Released: 2015-12-02 
• Deposition Author(s): Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H.
• Funding Organization(s): Japan Society for the Promotion of Science; Ministry of Education, Culture, Sports, Science and Technology 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.005 Å
• R-Value Free: 0.289 
• R-Value Work: 0.203 

Literature

Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome

Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H.

(2015) Sci Rep 5: 16330-16330

• PubMed: 26573481 
• DOI: 10.1038/srep16330
• Primary Citation of Related Structures:  
  4YM6


• PubMed Abstract: 
  

UV-DDB, an initiation factor for the nucleotide excision repair pathway, recognizes 6-4PP lesions through a base flipping mechanism. As genomic DNA is almost entirely accommodated within nucleosomes, the flipping of the 6-4PP bases is supposed to be extremely difficult if the lesion occurs in a nucleosome, especially on the strand directly contacting the histone surface. Here we report that UV-DDB binds efficiently to nucleosomal 6-4PPs that are rotationally positioned on the solvent accessible or occluded surface. We determined the crystal structures of nucleosomes containing 6-4PPs in these rotational positions, and found that the 6-4PP DNA regions were flexibly disordered, especially in the strand exposed to the solvent. This characteristic of 6-4PP may facilitate UV-DDB binding to the damaged nucleosome. We present the first atomic-resolution pictures of the detrimental DNA cross-links of neighboring pyrimidine bases within the nucleosome, and provide the mechanistic framework for lesion recognition by UV-DDB in chromatin.

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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	Mutation(s): 0  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	Mutation(s): 0  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	Mutation(s): 0  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	Mutation(s): 0  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
144 mer-DNA	I	144	Homo sapiens

Entity ID: 6
Molecule	Chains	Length	Organism
144-mer DNA	J	144	Homo sapiens

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
T64	I, J	DNA linking	C20 H28 N4 O15 P2		DT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.005 Å
• R-Value Free: 0.289 
• R-Value Work: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 104.193	α = 90.00
b = 109.356	β = 90.00
c = 174.417	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-03-06 
• Released Date: 2015-12-02 
• Deposition Author(s): Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	25250023
Ministry of Education, Culture, Sports, Science and Technology	Japan	25131720
Ministry of Education, Culture, Sports, Science and Technology	Japan	25116002

Revision History 

• Version 1.0: 2015-12-02
  Type: Initial release