2NQB

Drosophila Nucleosome Structure

• PDB DOI: https://doi.org/10.2210/pdb2NQB/pdb
• NAKB: 2NQB

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Homo sapiens, Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-10-30 Released: 2007-09-11 
• Deposition Author(s): Luger, K., Chakravarthy, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.254 
• R-Value Work: 0.223 

Literature

Comparative analysis of nucleosome structures from different species.

Chakravarthy, S., Luger, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A7B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 197.35 kDa 
• Atom Count: 12,294 
• Modelled Residue Count: 1,054 
• Deposited Residue Count: 1,260 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	C [auth A], G [auth E]	135	Drosophila melanogaster	Mutation(s): 0  Gene Names: His4
UniProt
Find proteins for P02299 (Drosophila melanogaster) Explore P02299  Go to UniProtKB:  P02299

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth B], H [auth F]	103	Drosophila melanogaster	Mutation(s): 0  Gene Names: His2A
UniProt
Find proteins for P84040 (Drosophila melanogaster) Explore P84040  Go to UniProtKB:  P84040

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	E [auth C], I [auth G]	123	Drosophila melanogaster	Mutation(s): 0  Gene Names: His2B
UniProt
Find proteins for P84051 (Drosophila melanogaster) Explore P84051  Go to UniProtKB:  P84051

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	F [auth D], J [auth H]	123	Drosophila melanogaster	Mutation(s): 1
UniProt
Find proteins for P02283 (Drosophila melanogaster) Explore P02283  Go to UniProtKB:  P02283

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: 2.30 Å
• R-Value Free: 0.254 
• R-Value Work: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.143	α = 90
b = 109.581	β = 90
c = 182.045	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-11 
Deposition Author(s): Luger, K., Chakravarthy, S.

Revision History  

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description