5XAH

Crystal structure of human Importin4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.004 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Integrative Structural Investigation on the Architecture of Human Importin4_Histone H3/H4_Asf1a Complex and Its Histone H3 Tail Binding

Yoon, J.Kim, S.J.An, S.Cho, S.Leitner, A.Jung, T.Aebersold, R.Hebert, H.Cho, U.S.Song, J.J.

(2018) J. Mol. Biol. 430: 822-841

  • DOI: 10.1016/j.jmb.2018.01.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Importin4 transports histone H3/H4 in complex with Asf1a to the nucleus for chromatin assembly. Importin4 recognizes the nuclear localization sequence located at the N-terminal tail of histones. Here, we analyzed the structures and interactions of hu ...

    Importin4 transports histone H3/H4 in complex with Asf1a to the nucleus for chromatin assembly. Importin4 recognizes the nuclear localization sequence located at the N-terminal tail of histones. Here, we analyzed the structures and interactions of human Importin4, histones and Asf1a by cross-linking mass spectrometry, X-ray crystallography, negative-stain electron microscopy, small-angle X-ray scattering and integrative modeling. The cross-linking mass spectrometry data showed that the C-terminal region of Importin4 was extensively cross-linked with the histone H3 tail. We determined the crystal structure of the C-terminal region of Importin4 bound to the histone H3 peptide, thus revealing that the acidic patch in Importin4 accommodates the histone H3 tail, and that histone H3 Lys14 contributes to the interaction with Importin4. In addition, we show that Asf1a modulates the binding of histone H3/H4 to Importin4. Furthermore, the molecular architecture of the Importin4_histone H3/H4_Asf1a complex was produced through an integrative modeling approach. Overall, this work provides structural insights into how Importin4 recognizes histones and their chaperone complex.


    Related Citations: 
    • Structural insights into the Architecture of human Importin4_Histone H3/H4_Asfla complex and its histone H3 tail binding
      Yoon, J.,Song, J.J.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.,Department of Biological Chemistry, University of Michigan Medical School, 1150 W. Medical Center Dr., SPC 5606, Ann Arbor, MI 48109, USA.,Department of Biological Sciences, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; Department of Biosciences and Nutrition, Karolinska Institutet, and School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Novum, SE-141 57, Sweden.,Department of Biological Sciences, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea. Electronic address: songj@kaist.ac.kr.,Department of Biological Sciences, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.,Department of Biosciences and Nutrition, Karolinska Institutet, and School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Novum, SE-141 57, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Importin-4
A, B, C, D
416Homo sapiensMutation(s): 0 
Gene Names: IPO4 (IMP4B, RANBP4)
Find proteins for Q8TEX9 (Homo sapiens)
Go to Gene View: IPO4
Go to UniProtKB:  Q8TEX9
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.004 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.920α = 90.00
b = 110.769β = 106.50
c = 126.820γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data scaling
HKLdata scaling
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-03-13 
  • Released Date: 2018-02-14 
  • Deposition Author(s): Song, J.J., Yoon, J.

Funding OrganizationLocationGrant Number
National Research Foundation (NRF)Korea, Republic Of2016R1A2B3006293,2016K1A1A2912057

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references