Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A7B1 Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 

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

Macromolecule Content

• Total Structure Weight: 202.81 kDa 
• Atom Count: 12198 
• Modelled Residue Count: 1050 
• Deposited Residue Count: 1306 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

3AFA

The human nucleosome structure

• DOI: 10.2210/pdb3AFA/pdb
• NDB: NA0467

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-24 Released: 2010-05-26 
• Deposition Author(s): Tachiwana, H., Kagawa, W., Osakabe, A., Koichiro, K., Shiga, T., Kimura, H., Kurumizaka, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.270 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 

Literature

Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T

Tachiwana, H., Kagawa, W., Osakabe, A., Kawaguchi, K., Shiga, T., Hayashi-Takanaka, Y., Kimura, H., Kurumizaka, H.

(2010) Proc Natl Acad Sci U S A 107: 10454-10459

• PubMed: 20498094 
• DOI: 10.1073/pnas.1003064107
• Primary Citation of Related Structures:  
  3A6N, 3AFA


• PubMed Abstract: 
  

A histone H3 variant, H3T, is highly expressed in the testis, suggesting that it may play an important role in the chromatin reorganization required for meiosis and/or spermatogenesis. In the present study, we found that the nucleosome containing human H3T is significantly unstable both in vitro and in vivo, as compared to the conventional nucleosome containing H3.1. The crystal structure of the H3T nucleosome revealed structural differences in the H3T regions on both ends of the central alpha2 helix, as compared to those of H3.1. The H3T-specific residues (Met71 and Val111) are the source of the structural differences observed between H3T and H3.1. A mutational analysis revealed that these residues are responsible for the reduced stability of the H3T-containing nucleosome. These physical and structural properties of the H3T-containing nucleosome may provide the basis of chromatin reorganization during spermatogenesis.

---

Organizational Affiliation: 

Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E	139	Homo sapiens	Mutation(s): 0  Gene Names:  H3.1, H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS:  P68431 GTEx:  ENSG00000197409ENSG00000197153ENSG00000278828ENSG00000275714ENSG00000273983ENSG00000274750ENSG00000275379ENSG00000277775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	106	Homo sapiens	Mutation(s): 0  Gene Names:  H4, H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS:  P62805 GTEx:  ENSG00000274618ENSG00000197238ENSG00000197837ENSG00000158406ENSG00000278705ENSG00000197061ENSG00000270882ENSG00000270276ENSG00000273542ENSG00000277157ENSG00000276966ENSG00000276180ENSG00000278637ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G	133	Homo sapiens	Mutation(s): 0  Gene Names: H2A, H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS:  P04908 GTEx:  ENSG00000277075ENSG00000278463

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H	129	Homo sapiens	Mutation(s): 0  Gene Names: H2B, H2BC11, H2BFR, HIST1H2BJ
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899
NIH Common Fund Data Resources
PHAROS:  P06899 GTEx:  ENSG00000124635

Entity ID: 5
Molecule	Chains	Length	Organism	Image
146-MER DNA	I, J	146	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	D, I, J	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	A, C, E, G	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.270 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.839	α = 90
b = 109.509	β = 90
c = 180.919	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-24 
• Released Date: 2010-05-26 
Deposition Author(s): Tachiwana, H., Kagawa, W., Osakabe, A., Koichiro, K., Shiga, T., Kimura, H., Kurumizaka, H.

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-07-18
  Changes: Structure summary