Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2BCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A7B1 

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

Macromolecule Content

• Total Structure Weight: 201.85 kDa 
• Atom Count: 11899 
• Residue Count: 1040 
• 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
• Mutation(s): No 


• 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: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

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
• Structures With Same Primary Citation


• 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: 

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.3C	A, E	138	Homo sapiens	Mutation(s): 0  Gene Names: H3F3C, H3-5
Find proteins for Q6NXT2 (Homo sapiens) Go to UniProtKB:  Q6NXT2
NIH Common Fund Data Resources
PHAROS  Q6NXT2 GTEx  ENSG00000188375

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F	106	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
Find proteins for P62805 (Homo sapiens) Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805 GTEx  ENSG00000274618GTEx  ENSG00000197238GTEx  ENSG00000197837GTEx  ENSG00000158406GTEx  ENSG00000278705GTEx  ENSG00000197061GTEx  ENSG00000270882GTEx  ENSG00000270276GTEx  ENSG00000273542GTEx  ENSG00000277157GTEx  ENSG00000276966GTEx  ENSG00000276180GTEx  ENSG00000278637GTEx  ENSG00000275126

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, H2BC11
Find proteins for P06899 (Homo sapiens) Go to UniProtKB:  P06899
NIH Common Fund Data Resources
PHAROS  P06899 GTEx  ENSG00000124635

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, H2AFM, HIST1H2AE, H2AFA, H2AC4, H2AC8
Find proteins for P04908 (Homo sapiens) Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS  P04908 GTEx  ENSG00000277075GTEx  ENSG00000278463

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: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.891	α = 90
b = 109.129	β = 90
c = 174.492	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
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
  Changes: Data collection, Derived calculations