1ZR5

Crystal structure of the macro-domain of human core histone variant macroH2A1.2

• PDB DOI: https://doi.org/10.2210/pdb1ZR5/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-05-19 Released: 2005-06-21 
• Deposition Author(s): Kustatscher, G., Hothorn, M., Pugieux, C., Scheffzek, K., Ladurner, A.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.277 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Starting Model: experimental

Literature

Splicing regulates NAD metabolite binding to histone macroH2A.

Kustatscher, G., Hothorn, M., Pugieux, C., Scheffzek, K., Ladurner, A.G.

(2005) Nat Struct Mol Biol 12: 624-625

• PubMed: 15965484 
• DOI: https://doi.org/10.1038/nsmb956
• Primary Citation of Related Structures:  
  1ZR5, 2FXK


• PubMed Abstract: 
  

  Histone macroH2A is a hallmark of mammalian heterochromatin. Here we show that human macroH2A1.1 binds the SirT1-metabolite O-acetyl-ADP-ribose (OAADPR) through its macro domain. The 1.6-A crystal structure and mutants reveal how the metabolite is recognized. Mutually exclusive exon use in the gene H2AFY produces macroH2A1.2, whose tissue distribution differs. MacroH2A1.2 shows only subtle structural changes but cannot bind nucleotides. Alternative splicing may thus regulate the binding of nicotinamide adenine dinucleotide (NAD) metabolites to chromatin.

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Organizational Affiliation: 

Gene Expression Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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.

Macromolecule Content

• Total Structure Weight: 45.41 kDa 
• Atom Count: 2,855 
• Modelled Residue Count: 376 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H2AFY protein	A, B	214	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75367 (Homo sapiens) Explore O75367  Go to UniProtKB:  O75367
PHAROS:  O75367 GTEx:  ENSG00000113648

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 0.277 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.549	α = 90
b = 72.258	β = 90
c = 144.641	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-21 
Deposition Author(s): Kustatscher, G., Hothorn, M., Pugieux, C., Scheffzek, K., Ladurner, A.G.

Revision History  

• Version 1.0: 2005-06-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Refinement description