Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 8-mer -A6B2 

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

Macromolecule Content

• Total Structure Weight: 201845.95 
• Atom Count: 11899 
• Residue Count: 1304 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

4Z5T

The nucleosome containing human H3.5

• DOI: 10.2210/pdb4Z5T/pdb
• NDB: 4Z5T

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


• Deposited: 2015-04-03 Released: 2016-02-10 
• Deposition Author(s): Urahama, T., Harada, A., Maehara, K., Horikoshi, N., Sato, K., Sato, Y., Shiraishi, K., Sugino, N., Osakabe, A., Tachiwana, H., Kagawa, W., Kimura, H., Ohkawa, Y., Kurumizaka, H.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology 

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.269 
• R-Value Work: 0.228 

Literature

Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis.

Urahama, T., Harada, A., Maehara, K., Horikoshi, N., Sato, K., Sato, Y., Shiraishi, K., Sugino, N., Osakabe, A., Tachiwana, H., Kagawa, W., Kimura, H., Ohkawa, Y., Kurumizaka, H.

(2016) Epigenetics Chromatin 9: 2-2

• PubMed: 26779285 
• DOI: 10.1186/s13072-016-0051-y


• PubMed Abstract: 
  

Human histone H3.5 is a non-allelic H3 variant evolutionally derived from H3.3. The H3.5 mRNA is highly expressed in human testis. However, the function of H3.5 has remained poorly understood.

---

Organizational Affiliation: 

Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506 Japan.,Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582 Japan.,Faculty of Medicine and Health Sciences, Yamaguchi University, 1-1-1 Minami-Kogushi, Ube, 755-8505 Japan.,Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Institute for Medical-oriented Structural Biology, 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 H3.3C	A, E	138	Homo sapiens	Mutation(s): 0  Gene Names: H3F3C
Find proteins for Q6NXT2 (Homo sapiens) Go to Gene View: H3F3C Go to UniProtKB:  Q6NXT2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F	106	Homo sapiens	Mutation(s): 0  Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens) 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: H2AC4, H2AC8 (H2AFM, HIST1H2AB, H2AFA, HIST1H2AE)
Find proteins for P04908 (Homo sapiens) 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: H2BC11 (H2BFR, HIST1H2BJ)
Find proteins for P06899 (Homo sapiens) Go to UniProtKB:  P06899

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: 2.8 Å
• R-Value Free: 0.269 
• R-Value Work: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 104.891	α = 90.00
b = 109.129	β = 90.00
c = 174.492	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-04-03 
• Released Date: 2016-02-10 
• Deposition Author(s): Urahama, T., Harada, A., Maehara, K., Horikoshi, N., Sato, K., Sato, Y., Shiraishi, K., Sugino, N., Osakabe, A., Tachiwana, H., Kagawa, W., Kimura, H., Ohkawa, Y., Kurumizaka, H.

---

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology	Japan	25116002
Ministry of Education, Culture, Sports, Science and Technology	Japan	25116005
Ministry of Education, Culture, Sports, Science and Technology	Japan	25131706
Ministry of Education, Culture, Sports, Science and Technology	Japan	26116521

Revision History 

• Version 1.0: 2016-02-10
  Type: Initial release
• Version 1.1: 2020-02-19
  Type: Data collection, Derived calculations