+Open data
-Basic information
Entry | Database: PDB / ID: 7apx | |||||||||
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Title | yeast THO-Sub2 complex | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN / yeast THO complex S. cerevisiae THO-Sub2 the transcription-export (TREX) complex | |||||||||
Function / homology | Function and homology information nucleoplasmic THO complex / cellular response to azide / THO complex / THO complex part of transcription export complex / positive regulation of transcription elongation by RNA polymerase I / transcription export complex / Cdc73/Paf1 complex / mRNA 3'-end processing / positive regulation of transcription by RNA polymerase I / subtelomeric heterochromatin formation ...nucleoplasmic THO complex / cellular response to azide / THO complex / THO complex part of transcription export complex / positive regulation of transcription elongation by RNA polymerase I / transcription export complex / Cdc73/Paf1 complex / mRNA 3'-end processing / positive regulation of transcription by RNA polymerase I / subtelomeric heterochromatin formation / transcription-coupled nucleotide-excision repair / mRNA export from nucleus / stress granule assembly / transcription elongation by RNA polymerase II / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / chromosome, telomeric region / DNA recombination / nucleic acid binding / molecular adaptor activity / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Schuller, S.K. / Schuller, J.M. / Prabu, R.J. / Baumgartner, M. / Bonneau, F. / basquin, J. / Conti, E. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Elife / Year: 2020 Title: Structural insights into the nucleic acid remodeling mechanisms of the yeast THO-Sub2 complex. Authors: Sandra K Schuller / Jan M Schuller / J Rajan Prabu / Marc Baumgärtner / Fabien Bonneau / Jérôme Basquin / Elena Conti / Abstract: The yeast THO complex is recruited to active genes and interacts with the RNA-dependent ATPase Sub2 to facilitate the formation of mature export-competent messenger ribonucleoprotein particles and to ...The yeast THO complex is recruited to active genes and interacts with the RNA-dependent ATPase Sub2 to facilitate the formation of mature export-competent messenger ribonucleoprotein particles and to prevent the co-transcriptional formation of RNA:DNA-hybrid-containing structures. How THO-containing complexes function at the mechanistic level is unclear. Here, we elucidated a 3.4 Å resolution structure of THO-Sub2 by cryo-electron microscopy. THO subunits Tho2 and Hpr1 intertwine to form a platform that is bound by Mft1, Thp2, and Tex1. The resulting complex homodimerizes in an asymmetric fashion, with a Sub2 molecule attached to each protomer. The homodimerization interfaces serve as a fulcrum for a seesaw-like movement concomitant with conformational changes of the Sub2 ATPase. The overall structural architecture and topology suggest the molecular mechanisms of nucleic acid remodeling during mRNA biogenesis. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7apx.cif.gz | 509.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7apx.ent.gz | 383.8 KB | Display | PDB format |
PDBx/mmJSON format | 7apx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7apx_validation.pdf.gz | 873.8 KB | Display | wwPDB validaton report |
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Full document | 7apx_full_validation.pdf.gz | 911.2 KB | Display | |
Data in XML | 7apx_validation.xml.gz | 70 KB | Display | |
Data in CIF | 7apx_validation.cif.gz | 112.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/7apx ftp://data.pdbj.org/pub/pdb/validation_reports/ap/7apx | HTTPS FTP |
-Related structure data
Related structure data | 11859MC 7aqoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-THO complex subunit ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 186067.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c Gene: THO2, LDB5, RLR1, ZRG13, YNL139C, N1209, N1835, YNL139C Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53552 |
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#2: Protein | Mass: 84544.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HPR1, YDR138W, YD9302.14 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17629 |
#3: Protein | Mass: 30340.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: THP2, YHR167W / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O13539 |
#4: Protein | Mass: 45055.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MFT1, YML062C / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33441 |
-Protein , 2 types, 2 molecules EF
#5: Protein | Mass: 42315.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TEX1, YNL253W, N0860 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53851 |
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#6: Protein | Mass: 45521.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SUB2, YDL084W / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q07478, RNA helicase |
-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: yeast THO-Sub2 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 431 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 298657 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |