5NL0

Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.4 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.240

Literature

Macromolecules
Sequence Display for 5NL0

Classification: CHROMATIN BINDING PROTEIN / DNA

Total Structure Weight: 426621.03


Macromolecule Entities
Molecule Chains Length Organism Details
Histone H3.2 A, E, K 135 Xenopus laevis Mutation: G102A
Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as a molecular replacement template (because it had the same 601L DNA sequence and therefore was the closest high-res structure available).
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H4 B, F, L 102 Xenopus laevis Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as a molecular replacement template (because it had the same 601L DNA sequence and therefore was the closest high-res structure available).
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2A type 1 C, G, M 129 Xenopus laevis Mutation: G99R, A123S
Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as a molecular replacement template (because it had the same 601L DNA sequence and therefore was the closest high-res structure available).
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2B 1.1 D, H, N 122 Xenopus laevis Mutation: S29T
Details: The core histones in the uploaded coordinates are those from X. laevis while those in the crystal are human. The reason for the discrepancy is that the structure was solved using pdb 3UT9 as a molecular replacement template (because it had the same 601L DNA sequence and therefore was the closest high-res structure available).
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H1.0-B Z 196 Xenopus laevis Details: Only the H1.0b globular domain was visible in the structure. The coordinates of this chain are those of a homology model built from chicken GH5 (pdb 1HST).
Gene Name(s): h1f0-b
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (197-MER) I, S 197 Synthetic construct There are only 193 bp in the structure whereas there are 197 bp in the crystal; putatively this could be because two base pairs at the tip of each linker are denatured and therefore not visible.
DNA (197-MER) J, T 197 Synthetic construct There are only 193 bp in the structure whereas there are 197 bp in the crystal; putatively this could be because two base pairs at the tip of each linker are denatured and therefore not visible.


Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.4 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.240
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 61.72 α = 90.00
b = 405.74 β = 90.00
c = 348.16 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-04-03
  • Released Date: 2017-05-17
  • Deposition author(s): Garcia-Saez, I., Petosa, C., Dimitrov, S.

Revision History

  • Version 1_0: 2017-05-17

    Type: Initial release

  • Version 1_1: 2017-08-30

    Type: Author supporting evidence