5F99

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 co ...

    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.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology Zurich, 8093 Zurich, Switzerland richmond@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G
129Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
122Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Protein Feature View
  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
103Xenopus laevisMutation(s): 1 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsLengthOrganism
DNA (147-MER)I147Mouse mammary tumor virus

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Entity ID: 6
MoleculeChainsLengthOrganism
DNA (147-MER)J147Mouse mammary tumor virus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A, C, E, G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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 = 107.873α = 90
b = 178.915β = 90
c = 109.061γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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