6JR1

Crystal structure of the human nucleosome phased with 16 selenium atoms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure determination of the nucleosome core particle by selenium SAD phasing.

Saotome, M.Horikoshi, N.Urano, K.Kujirai, T.Yuzurihara, H.Kurumizaka, H.Kagawa, W.

(2019) Acta Crystallogr D Struct Biol 75: 930-936

  • DOI: 10.1107/S2059798319012713
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The eukaryotic genome is compacted inside the nucleus of the cell in the form called chromatin. The fundamental unit of chromatin is the nucleosome, which contains four types of histones (H3, H4, H2A and H2B) and approximately 150 base pairs of DNA w ...

    The eukaryotic genome is compacted inside the nucleus of the cell in the form called chromatin. The fundamental unit of chromatin is the nucleosome, which contains four types of histones (H3, H4, H2A and H2B) and approximately 150 base pairs of DNA wrapped around the histone complex. The structure of the nucleosome is highly conserved across several eukaryotic species, and molecular replacement has been the primary phasing method used to solve nucleosome structures by X-ray crystallography. However, there is currently no simple, widely applicable experimental phasing method for the nucleosome. In the present study, it is demonstrated that selenomethionine-incorporated histones H3, H2A and H2B can be reconstituted into nucleosomes and crystallized for structural determination. Unexpectedly, it was found that the nucleosome can be phased with a relatively small number of Se atoms. The structures of nucleosome core particles containing 12 and 16 Se atoms were solved by SAD phasing at 2.5 and 2.4 Å resolution, respectively. The present study demonstrates a simple method for determining nucleosome structures by experimental phasing, which may be particularly useful for noncanonical structures that cannot be solved by molecular replacement.


    Organizational Affiliation

    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,Department of Chemistry, Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
A, E
139Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
106Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/E
C, G
133Homo sapiensMutation(s): 2 
Gene Names: H2AC4, H2AC8 (H2AFM, HIST1H2AB, H2AFA, HIST1H2AE)
Find proteins for P04908 (Homo sapiens)
Go to UniProtKB:  P04908
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
D, H
129Homo sapiensMutation(s): 2 
Gene Names: H2BC11 (H2BFR, HIST1H2BJ)
Find proteins for P06899 (Homo sapiens)
Go to UniProtKB:  P06899
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (146-MER)I,J146Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
E, I, J
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, C, E, G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, C, D, E, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 99.461α = 90.00
b = 108.539β = 90.00
c = 170.462γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP24570138
Japan Society for the Promotion of ScienceJapanJP26116521
Japan Society for the Promotion of ScienceJapanJP16H01316
Japan Society for the Promotion of ScienceJapanJP18H05534
Japan Society for the Promotion of ScienceJapanJP17H01408
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101076

Revision History 

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-23
    Type: Data collection, Database references