3X1V

Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

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

  • 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 transcrip ...

    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.


    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: kumarevel.thirumananseri@riken.jp.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1AE135Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF102Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/ECG129Homo sapiensMutation(s): 0 
Gene Names: H2AH2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
NIH Common Fund Data Resources
PHAROS  P04908
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-ADH126Mus musculusMutation(s): 0 
Gene Names: H2BAH2bc1Hist1h2baTh2b
Find proteins for P70696 (Mus musculus)
Explore P70696 
Go to UniProtKB:  P70696
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (146-MER)I, J146synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
D, G, I, J
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B, D, I, J
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.327α = 90
b = 108.471β = 90
c = 168.677γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description