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Yorodumi- PDB-8h5b: The cryo-EM structure of nuclear transport receptor Kap114p compl... -
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-Basic information
Entry | Database: PDB / ID: 8h5b | ||||||
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Title | The cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box binding protein | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / nuclear transport receptor Kap114p / yeast TATA-box binding protein | ||||||
Function / homology | Function and homology information TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / DNA binding, bending / nuclear import signal receptor activity ...TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / DNA binding, bending / nuclear import signal receptor activity / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II transcribes snRNA genes / NLS-bearing protein import into nucleus / transcription factor TFIID complex / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II general transcription initiation factor activity / RNA Polymerase II Pre-transcription Events / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / mRNA transport / RNA polymerase II core promoter sequence-specific DNA binding / nuclear pore / RNA polymerase II preinitiation complex assembly / DNA-templated transcription initiation / small GTPase binding / protein import into nucleus / disordered domain specific binding / nuclear envelope / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.03 Å | ||||||
Authors | Hsia, K.C. / Liao, C.C. / Wang, C.H. / Wu, Y.M. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural convergence endows nuclear transport receptor Kap114p with a transcriptional repressor function toward TATA-binding protein. Authors: Chung-Chi Liao / Yi-Sen Wang / Wen-Chieh Pi / Chun-Hsiung Wang / Yi-Min Wu / Wei-Yi Chen / Kuo-Chiang Hsia / 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 ...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). Remarkably, Kap114p wraps around the yTBP 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h5b.cif.gz | 199.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h5b.ent.gz | 156.5 KB | Display | PDB format |
PDBx/mmJSON format | 8h5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h5b_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8h5b_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8h5b_validation.xml.gz | 46.7 KB | Display | |
Data in CIF | 8h5b_validation.cif.gz | 68.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/8h5b ftp://data.pdbj.org/pub/pdb/validation_reports/h5/8h5b | HTTPS FTP |
-Related structure data
Related structure data | 34490MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 114019.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: KAP114, YGL241W, HRC1004 / Production host: Escherichia coli (E. coli) / References: UniProt: P53067 |
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#2: Protein | Mass: 20120.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: SPT15, BTF1, TBP1, YER148W / Production host: Escherichia coli (E. coli) / References: UniProt: P13393 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: nuclear transport receptor Kap114p complex with yeast TATA-box binding protein Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae S228 (yeast) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 15000 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212899 / Symmetry type: POINT |