Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5

Experimental Data Snapshot

  • Resolution: 5.53 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history


Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures.

Zhou, B.R.Jiang, J.Ghirlando, R.Norouzi, D.Sathish Yadav, K.N.Feng, H.Wang, R.Zhang, P.Zhurkin, V.Bai, Y.

(2018) J. Mol. Biol. 430: 3093-3110


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A, E, K, O
98Drosophila melanogasterMutation(s): 0 
Gene Names: His3, His3:CG31613, His3:CG33803, His3:CG33806, His3:CG33809, His3:CG33812, His3:CG33815, His3:CG33818, His3:CG33821, His3:CG33824, His3:CG33827, His3:CG33830, His3:CG33833, His3:CG33836, His3:CG33839, His3:CG33842, His3:CG33845, His3:CG33848, His3:CG33851, His3:CG33854, His3:CG33857, His3:CG33860, His3:CG33863, His3:CG33866
Find proteins for P02299 (Drosophila melanogaster)
Go to UniProtKB:  P02299
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F, L, P
82Drosophila melanogasterMutation(s): 0 
Gene Names: His4, His4r, His4:CG31611, His4:CG33869, His4:CG33871, His4:CG33873, His4:CG33875, His4:CG33877, His4:CG33879, His4:CG33881, His4:CG33883, His4:CG33885, His4:CG33887, His4:CG33889, His4:CG33891, His4:CG33893, His4:CG33895, His4:CG33897, His4:CG33899, His4:CG33901, His4:CG33903, His4:CG33905, His4:CG33907, His4:CG33909 (H4, H4r)
Find proteins for P84040 (Drosophila melanogaster)
Go to UniProtKB:  P84040
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G, M, Q
104Drosophila melanogasterMutation(s): 0 
Gene Names: His2A, His2A:CG31618, His2A:CG33808, His2A:CG33814, His2A:CG33817, His2A:CG33820, His2A:CG33823, His2A:CG33826, His2A:CG33829, His2A:CG33832, His2A:CG33835, His2A:CG33838, His2A:CG33841, His2A:CG33844, His2A:CG33847, His2A:CG33850, His2A:CG33862, His2A:CG33865 (H2a)
Find proteins for P84051 (Drosophila melanogaster)
Go to UniProtKB:  P84051
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B
D, H, N, R
94Drosophila melanogasterMutation(s): 0 
Gene Names: His2B, His2B:CG17949, His2B:CG33868, His2B:CG33870, His2B:CG33872, His2B:CG33874, His2B:CG33876, His2B:CG33878, His2B:CG33880, His2B:CG33882, His2B:CG33884, His2B:CG33886, His2B:CG33888, His2B:CG33890, His2B:CG33892, His2B:CG33894, His2B:CG33896, His2B:CG33898, His2B:CG33900, His2B:CG33902, His2B:CG33904, His2B:CG33906, His2B:CG33908, His2B:CG33910
Find proteins for P02283 (Drosophila melanogaster)
Go to UniProtKB:  P02283
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Histone H5
U, V
76Gallus gallusMutation(s): 0 
Find proteins for P02259 (Gallus gallus)
Go to UniProtKB:  P02259
Entity ID: 5
DNA (167-MER)I,S167synthetic construct
Entity ID: 6
DNA (167-MER)J,T167synthetic construct
Experimental Data & Validation

Experimental Data

  • Resolution: 5.53 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 65.926α = 100.79
b = 108.543β = 90.08
c = 180.770γ = 89.94
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release