3X1T

Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2aa and H2ba

• PDB DOI:  https://doi.org/10.2210/pdb3X1T/pdb
• NAKB: 3X1T

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): synthetic construct, Homo sapiens, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-27 Released: 2015-09-23 
• Deposition Author(s): Sivaraman, P., Kumarevel, T.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.266 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Literature

Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming

Padavattan, S., Shinagawa, T., Hasegawa, K., Kumasaka, T., Ishii, S., Kumarevel, T.

(2015) Biochem Biophys Res Commun 464: 929-935

• PubMed: 26188507 
• DOI: https://doi.org/10.1016/j.bbrc.2015.07.070
• Primary Citation of Related Structures:  
  3X1S, 3X1T, 3X1U, 3X1V


• PubMed Abstract: 
  

Histone variants TH2a and TH2b are highly expressed in testes, oocytes and zygotes. Our recent analysis suggested that these histone variants enhance the induced generation of pluripotent stem cells (iPSCs) when co-expressed along with four transcription factors, Oct3/4, Sox2, Klf4 and c-Myc (OSKM), and are associated with an open chromatin structure [1]. In the present study, we report the crystal structures of nucleosomes (NCPs) with the mouse histone variants, TH2a and TH2b. The structures revealed two significant changes, as compared to the canonical counterparts: fewer histone-DNA contacts and changes in dimer-dimer interactions between TH2a-TH2a' (L1-loop). In vivo studies with domain swapping and point mutants of the variants revealed that the residues in the histone tails and the TH2a-L1 loop are important for reprogramming. Taken together, our work indicates that the NCP variants with structural modifications and flexible tails are most likely important for enhanced reprogramming of functions.

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Organizational Affiliation: 

RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Structural Biology Laboratory, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan. Electronic address: [e-mail].

Biological Assembly 1  

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: 200.92 kDa 
• Atom Count: 12,181 
• Modelled Residue Count: 1,053 
• Deposited Residue Count: 1,274 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	C [auth A], G [auth E]	135	Homo sapiens	Mutation(s): 0  Gene Names:  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
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth B], H [auth F]	102	Homo sapiens	Mutation(s): 0  Gene Names:  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
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	E [auth C], I [auth G]	128	Mus musculus	Mutation(s): 0  Gene Names: H2ac1, Hist1h2aa
UniProt
Find proteins for Q8CGP4 (Mus musculus) Explore Q8CGP4  Go to UniProtKB:  Q8CGP4

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-A	F [auth D], J [auth H]	126	Mus musculus	Mutation(s): 0  Gene Names: H2bc1, Hist1h2ba, Th2b
UniProt
Find proteins for P70696 (Mus musculus) Explore P70696  Go to UniProtKB:  P70696

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	A [auth I], B [auth J]	146	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	AA [auth J], BA [auth J], HA [auth A], JA [auth D], K [auth I], KA [auth D], L [auth I], M [auth I], N [auth I], NA [auth G], O [auth I], P [auth I], Q [auth I], R [auth I], S [auth I], T [auth I], U [auth I], V [auth J], W [auth J], X [auth J], Y [auth J], Z [auth J]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	CA [auth J], DA [auth J], EA [auth J], FA [auth J], GA [auth J], IA [auth B], LA [auth D], MA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.266 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.771	α = 90
b = 109.597	β = 90
c = 181.597	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-23 
Deposition Author(s): Sivaraman, P., Kumarevel, T.S.

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release