3T30 | pdb_00003t30

Human nucleoplasmin (Npm2): a histone chaperone in oocytes and early embryos


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.243 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure and function of human nucleoplasmin (npm2): a histone chaperone in oocytes and embryos.

Platonova, O.Akey, I.V.Head, J.F.Akey, C.W.

(2011) Biochemistry 50: 8078-8089

  • DOI: https://doi.org/10.1021/bi2006652
  • Primary Citation Related Structures: 
    3T30

  • PubMed Abstract: 

    Human Npm2 is an ortholog of Xenopus nucleoplasmin (Np), a chaperone that binds histones. We have determined the crystal structure of a truncated Npm2-core at 1.9 Å resolution and show that the N-terminal domains of Npm2 and Np form similar pentamers. This allowed us to model an Npm2 decamer which may be formed by hydrogen bonds between quasi-conserved residues in the interface between two pentamers. Interestingly, the Npm2 pentamer lacks a prototypical A1-acidic tract in each of its subunits. This feature may be responsible for the inability of Npm2-core to bind histones. However, Npm2 with a large acidic tract in its C-terminal tail (Npm2-A2) is able to bind histones and form large complexes. Fluorescence resonance energy transfer experiments and biochemical analysis of loop mutations support the premise that nucleoplasmins form decamers when they bind H2A-H2B dimers and H3-H4 tetramers simultaneously. In the absence of histone tetramers, these chaperones bind H2A-H2B dimers with a single pentamer forming the central hub. When taken together, our data provide insights into the mechanism of histone binding by nucleoplasmins.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany St., Boston, Massachusetts 02118-2526, USA.

Macromolecule Content 

  • Total Structure Weight: 123.94 kDa 
  • Atom Count: 7,862 
  • Modeled Residue Count: 922 
  • Deposited Residue Count: 1,100 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoplasmin-2110Homo sapiensMutation(s): 0 
Gene Names: NPM2
UniProt & NIH Common Fund Data Resources
Find proteins for Q86SE8 (Homo sapiens)
Explore Q86SE8 
Go to UniProtKB:  Q86SE8
PHAROS:  Q86SE8
GTEx:  ENSG00000158806 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86SE8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.243 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.03α = 90
b = 107.24β = 102.54
c = 108.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-11-30
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description