1YD9 | pdb_00001yd9

1.6A Crystal Structure of the Non-Histone Domain of the Histone Variant MacroH2A1.1.

• PDB DOI: https://doi.org/10.2210/pdb1YD9/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-23 Released: 2005-09-27 
• Deposition Author(s): Chakravarthy, S., Swamy, G.Y.S.K., Caron, C., Perche, P.Y., Pehrson, J.R., Khochbin, S., Luger, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.235 (DCC) 

Literature

Structural characterization of the histone variant macroH2A

Chakravarthy, S., Gundimella, S.K., Caron, C., Perche, P.Y., Pehrson, J.R., Khochbin, S., Luger, K.

(2005) Mol Cell Biol 25: 7616-7624

• PubMed: 16107708 
• DOI: https://doi.org/10.1128/MCB.25.17.7616-7624.2005
• Primary Citation Related Structures: 
  1U35, 1YD9


• PubMed Abstract: 
  

  macroH2A is an H2A variant with a highly unusual structural organization. It has a C-terminal domain connected to the N-terminal histone domain by a linker. Crystallographic and biochemical studies show that changes in the L1 loop in the histone fold region of macroH2A impact the structure and potentially the function of nucleosomes. The 1.6-A X-ray structure of the nonhistone region reveals an alpha/beta fold which has previously been found in a functionally diverse group of proteins. This region associates with histone deacetylases and affects the acetylation status of nucleosomes containing macroH2A. Thus, the unusual domain structure of macroH2A integrates independent functions that are instrumental in establishing a structurally and functionally unique chromatin domain.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, 80523-1870, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 82.94 kDa 
• Atom Count: 6,173 
• Modeled Residue Count: 750 
• Deposited Residue Count: 772 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Core histone macro-H2A.1	A, B, C, D	193	Rattus norvegicus	Mutation(s): 0  Gene Names: H2afy
UniProt
Find proteins for Q02874 (Rattus norvegicus) Explore Q02874  Go to UniProtKB:  Q02874

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU	E [auth A], F [auth B], G [auth C], H [auth D]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.235 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.114	α = 90
b = 89.791	β = 90
c = 95.679	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Chakravarthy, S., Swamy, G.Y.S.K., Caron, C., Perche, P.Y., Pehrson, J.R., Khochbin, S., Luger, K.

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations