2F8N | pdb_00002f8n

2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes

• PDB DOI: https://doi.org/10.2210/pdb2F8N/pdb
• NAKB: 2F8N

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Homo sapiens, Xenopus laevis, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-12-02 Released: 2006-05-23 
• Deposition Author(s): Chakravarthy, S., Luger, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.269 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.216 (DCC) 

Starting Model: experimental

Literature

Nucleosomes containing the histone domain of macroH2A: In vitro possibilities.

Chakravarthy, S., Luger, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A2B2C2D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A7B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 200.61 kDa 
• Atom Count: 12,066 
• Modeled Residue Count: 1,048 
• Deposited Residue Count: 1,288 
• Unique protein chains: 6
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	C [auth A], F [auth E]	136	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth B], G [auth F]	103	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone 3, H2ba	E [auth D]	126	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9D2U9 (Mus musculus) Explore Q9D2U9  Go to UniProtKB:  Q9D2U9

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B.1	H	123	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Core histone macro-H2A.1	I [auth G]	120	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

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	J [auth K]	149	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q8CGP6 (Mus musculus) Explore Q8CGP6  Go to UniProtKB:  Q8CGP6

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.269 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.216 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.145	α = 90
b = 109.272	β = 90
c = 176.273	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: 2006-05-23 
Deposition Author(s): Chakravarthy, S., Luger, K.

Revision History  

• Version 1.0: 2006-05-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description