Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2BCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A6B1C 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 199.29 kDa 
• Atom Count: 13349 
• Residue Count: 1097 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

5F99

X-ray Structure of the MMTV-A Nucleosome Core Particle

• DOI: 10.2210/pdb5F99/pdb
• NDB: 5F99

• Classification: DNA BINDING PROTEIN
• Organism(s): Xenopus laevis, Mouse mammary tumor virus
• Expression System: Escherichia coli BL21(DE3), Escherichia coli str. K-12 substr. DH10B
• Mutation(s): Yes 


• Deposited: 2015-12-09 Released: 2016-02-03 
• Deposition Author(s): Frouws, T.D., Richmond, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.252 
• R-Value Work: 0.175 

Literature

X-ray structure of the MMTV-A nucleosome core.

Frouws, T.D., Duda, S.C., Richmond, T.J.

(2016) Proc Natl Acad Sci U S A 113: 1214-1219

• PubMed: 26787910 
• DOI: 10.1073/pnas.1524607113
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The conformation of DNA bound in nucleosomes depends on the DNA sequence. Questions such as how nucleosomes are positioned and how they potentially bind sequence-dependent nuclear factors require near-atomic resolution structures of the nucleosome core containing different DNA sequences; despite this, only the DNA for two similar α-satellite sequences and a sequence (601) selected in vitro have been visualized bound in the nucleosome core. Here we report the 2.6-Å resolution X-ray structure of a nucleosome core particle containing the DNA sequence of nucleosome A of the 3'-LTR of the mouse mammary tumor virus (147 bp MMTV-A). To our knowledge, this is the first nucleosome core particle structure containing a promoter sequence and crystallized from Mg(2+) ions. It reveals sequence-dependent DNA conformations not seen previously, including kinking into the DNA major groove.

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Organizational Affiliation: 

Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology Zurich, 8093 Zurich, Switzerland [e-mail].

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A type 1	C, G	129	Xenopus laevis	Mutation(s): 0
Find proteins for P06897 (Xenopus laevis) Go to UniProtKB:  P06897

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B 1.1	D, H	122	Xenopus laevis	Mutation(s): 0
Find proteins for P02281 (Xenopus laevis) Go to UniProtKB:  P02281

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.2	A, E	135	Xenopus laevis	Mutation(s): 0
Find proteins for P84233 (Xenopus laevis) Go to UniProtKB:  P84233

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F	103	Xenopus laevis	Mutation(s): 1
Find proteins for P62799 (Xenopus laevis) Go to UniProtKB:  P62799

Entity ID: 5
Molecule	Chains	Length	Organism
DNA (147-MER)	I	147	Mouse mammary tumor virus

Entity ID: 6
Molecule	Chains	Length	Organism
DNA (147-MER)	J	147	Mouse mammary tumor virus

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	A, C, E, G	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.252 
• R-Value Work: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.873	α = 90
b = 178.915	β = 90
c = 109.061	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-12-09 
• Released Date: 2016-02-03 
Deposition Author(s): Frouws, T.D., Richmond, T.J.

Revision History 

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2016-02-10
  Changes: Database references