5W0V

Crystal structure of full-length Kluyveromyces lactis Kap123 with histone H4 1-34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.821 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-based nuclear import mechanism of histones H3 and H4 mediated by Kap123.

An, S.Yoon, J.Kim, H.Song, J.J.Cho, U.S.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.30244
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Kap123, a major karyopherin protein of budding yeast, recognizes the nuclear localization signals (NLSs) of cytoplasmic histones H3 and H4 and translocates them into the nucleus during DNA replication. Mechanistic questions include H3- and H4-NLS red ...

    Kap123, a major karyopherin protein of budding yeast, recognizes the nuclear localization signals (NLSs) of cytoplasmic histones H3 and H4 and translocates them into the nucleus during DNA replication. Mechanistic questions include H3- and H4-NLS redundancy toward Kap123 and the role of the conserved diacetylation of cytoplasmic H4 (K5ac and K12ac) in Kap123-mediated histone nuclear translocation. Here, we report crystal structures of full-length Kluyveromyces lactis Kap123 alone and in complex with H3- and H4-NLSs. Structures reveal the unique feature of Kap123 that possesses two discrete lysine-binding pockets for NLS recognition. Structural comparison illustrates that H3- and H4-NLSs share at least one of two lysine-binding pockets, suggesting that H3- and H4-NLSs are mutually exclusive. Additionally, acetylation of key lysine residues at NLS, particularly H4-NLS diacetylation, weakens the interaction with Kap123. These data support that cytoplasmic histone H4 diacetylation weakens the Kap123-H4-NLS interaction thereby facilitating histone Kap123-H3-dependent H3:H4/Asf1 complex nuclear translocation.


    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan Medical School, Michigan, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kap123
A, B
1116Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CMF0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CMF0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4 1-34
C, D
34Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HHF1, HHF2
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02309
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.821 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.170 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 78.793α = 79.59
b = 87.697β = 81.45
c = 101.623γ = 71.70
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release