5X7X

The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.227

Literature

Macromolecules
Sequence Display for 5X7X

Classification: STRUCTURAL PROTEIN / DNA

Total Structure Weight: 202934.33


Macromolecule Entities
Molecule Chains Length Organism Details
Histone H3.3 A, E 139 Homo sapiens Gene Name(s): H3F3A Gene View H3.3A H3F3 PP781 H3F3B Gene View H3.3B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H4 B, F 106 Homo sapiens Gene Name(s): HIST1H4A Gene View H4/A H4FA HIST1H4B Gene View H4/I H4FI HIST1H4C Gene View H4/G H4FG HIST1H4D Gene View H4/B H4FB HIST1H4E Gene View H4/J H4FJ HIST1H4F Gene View H4/C H4FC HIST1H4H Gene View H4/H H4FH HIST1H4I Gene View H4/M H4FM HIST1H4J Gene View H4/E H4FE HIST1H4K Gene View H4/D H4FD HIST1H4L Gene View H4/K H4FK HIST2H4A Gene View H4/N H4F2 H4FN HIST2H4 HIST2H4B Gene View H4/O H4FO HIST4H4 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2A type 1-B/E C, G 133 Homo sapiens Gene Name(s): HIST1H2AB Gene View H2AFM HIST1H2AE Gene View H2AFA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2B type 1-J D, H 129 Homo sapiens Gene Name(s): HIST1H2BJ Gene View H2BFR
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (146-MER) I, J 146 Homo sapiens

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MN
Query on MN

E, I, J MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, C, E, G CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.227
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 98.89 α = 90.00
b = 107.51 β = 90.00
c = 167.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-02-27
  • Released Date: 2017-04-19
  • Deposition author(s): Arimura, Y., Taguchi, H., Kurumizaka, H.

Revision History

  • Version 1_0: 2017-04-19

    Type: Initial release

  • Version 1_1: 2017-05-24

    Type: Database references

  • Version 1_2: 2017-10-11

    Type: Derived calculations

  • Version 2_0: 2017-10-18

    Type: Author supporting evidence, Polymer sequence