6AHO

Crystal structure of Kap114p


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Karyopherin Kap114p-mediated trans-repression controls ribosomal gene expression under saline stress.

Liao, C.C.Shankar, S.Pi, W.C.Chang, C.C.Ahmed, G.R.Chen, W.Y.Hsia, K.C.

(2020) EMBO Rep 21

  • DOI: 10.15252/embr.201948324
  • Primary Citation of Related Structures:  
    6AHO

  • PubMed Abstract: 
  • Nuclear accessibility of transcription factors controls gene expression, co-regulated by Ran-dependent nuclear localization and a competitive regulatory network. Here, we reveal that nuclear import factor-facilitated transcriptional repression attenu ...

    Nuclear accessibility of transcription factors controls gene expression, co-regulated by Ran-dependent nuclear localization and a competitive regulatory network. Here, we reveal that nuclear import factor-facilitated transcriptional repression attenuates ribosome biogenesis under chronic salt stress. Kap114p, one of the karyopherin-βs (Kap-βs) that mediates nuclear import of yeast TATA-binding protein (yTBP), exhibits a yTBP-binding affinity four orders of magnitude greater than its counterparts and suppresses binding of yTBP with DNA. Our crystal structure of Kap114p reveals an extensively negatively charged concave surface, accounting for high-affinity basic-protein binding. KAP114 knockout in yeast leads to a high-salt growth defect, with transcriptomic analyses revealing that Kap114p modulates expression of genes associated with ribosomal biogenesis by suppressing yTBP binding to target promoters, a trans-repression mechanism we attribute to reduced nuclear Ran levels under salinity stress. Our findings reveal that Ran integrates the nuclear transport pathway and transcription regulatory network, allowing yeast to respond to environmental stresses.


    Organizational Affiliation

    Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang-Ming University, Taipei, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Importin subunit beta-5A1009Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KAP114YGL241WHRC1004
Find proteins for P53067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53067 
Go to UniProtKB:  P53067
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.623α = 90
b = 116.623β = 90
c = 189.015γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan106-2311-B-001 -038 -MY3

Revision History 

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2020-06-17
    Changes: Database references
  • Version 1.3: 2020-07-01
    Changes: Database references
  • Version 1.4: 2020-07-22
    Changes: Database references