5J3V

Crystal structure of human Karyopherin-beta2 bound to the histone H3 tail

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2016-03-31 Released: 2016-09-21 
  • Deposition Author(s): Soniat, M., Chook, Y.M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; Welch Foundation Grant; Leukemia & Lymphoma Society; The University of Texas Southwestern Endowed Scholars Program 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Karyopherin-beta 2 Recognition of a PY-NLS Variant that Lacks the Proline-Tyrosine Motif.

Soniat, M.Chook, Y.M.

(2016) Structure 24: 1802-1809

  • DOI: 10.1016/j.str.2016.07.018

  • PubMed Abstract: 
  • Karyopherin-β2 or Transportin-1 binds proline-tyrosine nuclear localization signals (PY-NLSs) in its cargos. PY-NLSs are described by structural disorder, overall positive charge, and binding epitopes composed of an N-terminal hydrophobic or basic mo ...

    Karyopherin-β2 or Transportin-1 binds proline-tyrosine nuclear localization signals (PY-NLSs) in its cargos. PY-NLSs are described by structural disorder, overall positive charge, and binding epitopes composed of an N-terminal hydrophobic or basic motif and a C-terminal R-X2-5P-Y motif. The N-terminal tail of histone H3 binds Kapβ2 with high affinity but does not contain a recognizable PY-NLS. The crystal structure of the Kapβ2-H3 tail shows residues 11-27 of H3 binding to the PY-NLS site of Kapβ2. H3 residues 11TGGKAPRK18 bind the site for PY-NLS Epitope 1 (N-terminal hydrophobic/basic motif), which is most important for Kapβ2-binding. H3 residue Arg26 occupies the PY-NLS Epitope 2 position (usually arginine of R-X2-5P-Y) but PY-NLS Epitope 3 (proline-tyrosine motif) is missing in the H3 tail. Histone H3 thus provides an example of a PY-NLS variant with no proline-tyrosine or homologous proline-hydrophobic motif. The H3 tail uses a very strong Epitope 1 to compensate for loss of the often-conserved proline-tyrosine epitope.


    Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern, Dallas, TX 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transportin-1,Transportin-1
A, B
854Homo sapiensMutation(s): 0 
Gene Names: TNPO1 (KPNB2, MIP1, TRN)
Find proteins for Q92973 (Homo sapiens)
Go to Gene View: TNPO1
Go to UniProtKB:  Q92973
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3
C, D
17Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 150.296α = 90.00
b = 154.185β = 90.00
c = 192.661γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-3000data scaling
PHENIXrefinement
HKL-3000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM069909
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU01 GM98256-01
Welch Foundation GrantUnited StatesI-1532
Leukemia & Lymphoma SocietyUnited States--
The University of Texas Southwestern Endowed Scholars ProgramUnited States--

Revision History 

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations