2Z2R

Nucleosome assembly proteins I (NAP-1, 74-365)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A beta-hairpin comprising the nuclear localization sequence sustains the self-associated states of nucleosome assembly protein 1

Park, Y.J.McBryant, S.J.Luger, K.

(2008) J Mol Biol 375: 1076-1085

  • DOI: https://doi.org/10.1016/j.jmb.2007.11.031
  • Primary Citation of Related Structures:  
    2Z2R

  • PubMed Abstract: 

    The histone chaperone nucleosome assembly protein 1 (NAP1) is implicated in histone shuttling as well as nucleosome assembly and disassembly. Under physiological conditions, NAP1 dimers exist in a mixture of various high-molecular-weight oligomers whose size may be regulated by the cell cycle-dependent concentration of NAP1. Both the functional and structural significance of the observed oligomers are unknown. We have resolved the molecular mechanism by which yeast NAP1 (yNAP1) dimers oligomerize by applying x-ray crystallographic, hydrodynamic, and functional approaches. We found that an extended beta-hairpin that protrudes from the compact core of the yNAP1 dimer forms a stable beta-sheet with beta-hairpins of neighboring yNAP1 dimers. Disruption of the beta-hairpin (whose sequence is conserved among NAP1 proteins in various species) by the replacement of one or more amino acids with proline results in complete loss of yNAP1 dimer oligomerization. The in vitro functions of yNAP1 remain unaffected by the mutations. We have thus identified a conserved structural feature of NAP1 whose function, in addition to presenting the nuclear localization sequence, appears to be the formation of higher-order oligomers.


  • Organizational Affiliation

    Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleosome assembly protein
A, B
292Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NAP1
UniProt
Find proteins for P25293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25293 
Go to UniProtKB:  P25293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25293
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.260 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125α = 90
b = 125β = 90
c = 146.67γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description