1U35 | pdb_00001u35

Crystal structure of the nucleosome core particle containing the histone domain of macroH2A

• PDB DOI: https://doi.org/10.2210/pdb1U35/pdb
• NAKB: 1U35

• Classification: structural protein/DNA
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-07-20 Released: 2005-09-27 
• Deposition Author(s): Chakravarthy, S., Gundimella, 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: 3.00 Å
• R-Value Free: 
  0.260 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.205 (DCC) 

Starting Model: experimental

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 197.79 kDa 
• Atom Count: 12,053 
• Modeled Residue Count: 1,049 
• Deposited Residue Count: 1,262 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	C [auth A], G [auth E]	136	Mus musculus	Mutation(s): 0  Gene Names: H3FA, H3FC, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL
UniProt
Find proteins for P68433 (Mus musculus) Explore P68433  Go to UniProtKB:  P68433

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hist1h4i protein	D [auth B], H [auth F]	103	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62806 (Mus musculus) Explore P62806  Go to UniProtKB:  P62806
IMPC:  MGI:2448419MGI:2448420MGI:2448443

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
H2A histone family	E [auth C], I [auth G]	120	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for O75367 (Homo sapiens) Explore O75367  Go to UniProtKB:  O75367
PHAROS:  O75367 GTEx:  ENSG00000113648

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
histone 3, H2ba	F [auth D], J [auth H]	126	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9D2U9 (Mus musculus) Explore Q9D2U9  Go to UniProtKB:  Q9D2U9

Entity ID: 1
Molecule	Chains	Length	Organism	Image
alpha-satellite DNA	A [auth I], B [auth J]	146	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.260 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.205 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.505	α = 90
b = 109.598	β = 90
c = 175.989	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Chakravarthy, S., Gundimella, 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: 2021-10-20
  Changes: Database references
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description