8H5B | pdb_00008h5b

The cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box binding protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Structural convergence endows nuclear transport receptor Kap114p with a transcriptional repressor function toward TATA-binding protein.

Liao, C.C.Wang, Y.S.Pi, W.C.Wang, C.H.Wu, Y.M.Chen, W.Y.Hsia, K.C.

(2023) Nat Commun 14: 5518-5518

  • DOI: https://doi.org/10.1038/s41467-023-41206-9
  • Primary Citation Related Structures: 
    8H5B

  • PubMed Abstract: 

    The transcription factor TATA-box binding protein (TBP) modulates gene expression in nuclei. This process requires the involvement of nuclear transport receptors, collectively termed karyopherin-β (Kap-β) in yeast, and various regulatory factors. In previous studies we showed that Kap114p, a Kap-β that mediates nuclear import of yeast TBP (yTBP), modulates yTBP-dependent transcription. However, how Kap114p associates with yTBP to exert its multifaceted functions has remained elusive. Here, we employ single-particle cryo-electron microscopy to determine the structure of Kap114p in complex with the core domain of yTBP (yTBP C ). Remarkably, Kap114p wraps around the yTBP C N-terminal lobe, revealing a structure resembling transcriptional regulators in complex with TBP, suggesting convergent evolution of the two protein groups for a common function. We further demonstrate that Kap114p sequesters yTBP away from promoters, preventing a collapse of yTBP dynamics required for yeast responses to environmental stress. Hence, we demonstrate that nuclear transport receptors represent critical elements of the transcriptional regulatory network.


  • Organizational Affiliation
    • Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and National Defense Medical Center, Taipei, 11490, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 134.14 kDa 
  • Atom Count: 8,570 
  • Modeled Residue Count: 1,075 
  • Deposited Residue Count: 1,184 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Importin subunit beta-51,004Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KAP114YGL241WHRC1004
UniProt
Find proteins for P53067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53067 
Go to UniProtKB:  P53067
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53067
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TATA-box-binding protein180Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPT15BTF1TBP1YER148W
UniProt
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13393 
Go to UniProtKB:  P13393
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13393
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release