[English] 日本語
Yorodumi
- EMDB-34490: The cryo-EM structure of nuclear transport receptor Kap114p compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34490
TitleThe cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box binding protein
Map dataSharp map
Sample
  • Complex: nuclear transport receptor Kap114p complex with yeast TATA-box binding protein
    • Protein or peptide: Importin subunit beta-5
    • Protein or peptide: TATA-box-binding protein
Keywordsnuclear transport receptor Kap114p / yeast TATA-box binding protein / PROTEIN TRANSPORT
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
Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily ...Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
TATA-box-binding protein / Importin subunit beta-5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S228 (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.03 Å
AuthorsHsia KC / Liao CC / Wang CH / Wu YM
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: 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
DepositionOct 12, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34490.png

Downloads & links

-
Map

FileDownload / File: emd_34490.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.0251032 - 1.5200665
Average (Standard dev.)0.002034204 (±0.039869875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_34490_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharp map

Fileemd_34490_additional_1.map
AnnotationUnsharp map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_34490_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_34490_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : nuclear transport receptor Kap114p complex with yeast TATA-box bi...

EntireName: nuclear transport receptor Kap114p complex with yeast TATA-box binding protein
Components
  • Complex: nuclear transport receptor Kap114p complex with yeast TATA-box binding protein
    • Protein or peptide: Importin subunit beta-5
    • Protein or peptide: TATA-box-binding protein

-
Supramolecule #1: nuclear transport receptor Kap114p complex with yeast TATA-box bi...

SupramoleculeName: nuclear transport receptor Kap114p complex with yeast TATA-box binding protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S228 (yeast)

-
Macromolecule #1: Importin subunit beta-5

MacromoleculeName: Importin subunit beta-5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 114.019695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDINELIIGA QSADKHTREV AETQLLQWCD SDASQVFKAL ANVALQHEAS LESRQFALLS LRKLITMYWS PGFESYRSTS NVEIDVKDF IREVLLKLCL NDNENTKIKN GASYCIVQIS AVDFPDQWPQ LLTVIYDAIS HQHSLNAMSL LNEIYDDVVS E EMFFEGGI ...String:
MDINELIIGA QSADKHTREV AETQLLQWCD SDASQVFKAL ANVALQHEAS LESRQFALLS LRKLITMYWS PGFESYRSTS NVEIDVKDF IREVLLKLCL NDNENTKIKN GASYCIVQIS AVDFPDQWPQ LLTVIYDAIS HQHSLNAMSL LNEIYDDVVS E EMFFEGGI GLATMEIVFK VLNTETSTLI AKIAALKLLK ACLLQMSSHN EYDEASRKSF VSQCLATSLQ ILGQLLTLNF GN VDVISQL KFKSIIYENL VFIKNDFSRK HFSSELQKQF KIMAIQDLEN VTHINANVET TESEPLLETV HDCSIYIVEF LTS VCTLQF SVEEMNKIIT SLTILCQLSS ETREIWTSDF NTFVSKETGL AASYNVRDQA NEFFTSLPNP QLSLIFKVVS NDIE HSTCN YSTLESLLYL LQCILLNDDE ITGENIDQSL QILIKTLENI LVSQEIPELI LARAILTIPR VLDKFIDALP DIKPL TSAF LAKSLNLALK SDKELIKSAT LIAFTYYCYF AELDSVLGPE VCSETQEKVI RIINQVSSDA EEDTNGALME VLSQVI SYN PKEPHSRKEI LQAEFHLVFT ISSEDPANVQ VVVQSQECLE KLLDNINMDN YKNYIELCLP SFINVLDSNN ANNYRYS PL LSLVLEFITV FLKKKPNDGF LPDEINQYLF EPLAKVLAFS TEDETLQLAT EAFSYLIFNT DTRAMEPRLM DIMKVLER L LSLEVSDSAA MNVGPLVVAI FTRFSKEIQP LIGRILEAVV VRLIKTQNIS TEQNLLSVLC FLTCNDPKQT VDFLSSFQI DNTDALTLVM RKWIEAFEVI RGEKRIKENI VALSNLFFLN DKRLQKVVVN GNLIPYEGDL IITRSMAKKM PDRYVQVPLY TKIIKLFVS ELSFQSKQPN PEQLITSDIK QEVVNANKDD DNDDWEDVDD VLDYDKLKEY IDDDVDEEAD DDSDDITGLM D VKESVVQL LVRFFKEVAS KDVSGFHCIY ETLSDSERKV LSEALL

UniProtKB: Importin subunit beta-5

-
Macromolecule #2: TATA-box-binding protein

MacromoleculeName: TATA-box-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 20.120754 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGIVPTLQNI VATVTLGCRL DLKTVALHAR NAEYNPKRFA AVIMRIREPK TTALIFASGK MVVTGAKSED DSKLASRKYA RIIQKIGFA AKFTDFKIQN IVGSCDVKFP IRLEGLAFSH GTFSSYEPEL FPGLIYRMVK PKIVLLIFVS GKIVLTGAKQ R EEIYQAFE AIYPVLSEFR KM

UniProtKB: TATA-box-binding protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 25.0 µm / Nominal defocus min: 15.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212899
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more