2AYU | pdb_00002ayu

The structure of nucleosome assembly protein suggests a mechanism for histone binding and shuttling


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.280 (Depositor), 0.333 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.315 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2AYU

This is version 1.3 of the entry. See complete history

Literature

The structure of nucleosome assembly protein 1.

Park, Y.J.Luger, K.

(2006) Proc Natl Acad Sci U S A 103: 1248-1253

  • DOI: https://doi.org/10.1073/pnas.0508002103
  • Primary Citation Related Structures: 
    2AYU

  • PubMed Abstract: 

    Nucleosome assembly protein 1 (NAP-1) is an integral component in the establishment, maintenance, and dynamics of eukaryotic chromatin. It shuttles histones into the nucleus, assembles nucleosomes, and promotes chromatin fluidity, thereby affecting the transcription of many genes. The 3.0 A crystal structure of yeast NAP-1 reveals a previously uncharacterized fold with implications for histone binding and shuttling. A long alpha-helix is responsible for homodimerization via a previously uncharacterized antiparallel non-coiled-coil, and an alpha/beta domain is implicated in protein-protein interaction. A nuclear export sequence that is embedded in the dimerization helix is almost completely masked by an accessory domain that contains several target sites for casein kinase II. The four-stranded antiparallel beta-sheet that characterizes the alpha/beta domain is found in all histone chaperones, despite the absence of homology in sequence, structural context, or quaternary structure. To our knowledge, this is the first structure of a member of the large NAP family of proteins and suggests a mechanism by which the shuttling of histones to and from the nucleus is regulated.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.

Macromolecule Content 

  • Total Structure Weight: 47.93 kDa 
  • Atom Count: 2,323 
  • Modeled Residue Count: 283 
  • Deposited Residue Count: 417 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleosome assembly protein417Saccharomyces 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: 3.00 Å
  • R-Value Free:  0.280 (Depositor), 0.333 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.315 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.7α = 90
b = 86.7β = 90
c = 176.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Structure summary