+Open data
-Basic information
Entry | Database: PDB / ID: 7aqo | |||||||||
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Title | yeast THO-Sub2 complex dimer | |||||||||
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 / helicase activity / 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 S288C (yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 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 | 7aqo.cif.gz | 966.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aqo.ent.gz | 743.4 KB | Display | PDB format |
PDBx/mmJSON format | 7aqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aqo_validation.pdf.gz | 959 KB | Display | wwPDB validaton report |
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Full document | 7aqo_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7aqo_validation.xml.gz | 132.5 KB | Display | |
Data in CIF | 7aqo_validation.cif.gz | 210.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/7aqo ftp://data.pdbj.org/pub/pdb/validation_reports/aq/7aqo | HTTPS FTP |
-Related structure data
Related structure data | 11871MC 7apxC 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 ... , 3 types, 6 molecules GAHBID
#1: Protein | Mass: 184450.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: THO2, GI526_G0004933 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6A5Q535, UniProt: P53552*PLUS #2: Protein | Mass: 84544.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: HPR1, YDR138W, YD9302.14 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17629 #6: Protein | Mass: 45055.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: MFT1, YML062C / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33441 |
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-Protein , 3 types, 6 molecules KELFJC
#3: Protein | Mass: 42315.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: TEX1, GI526_G0004829, PACBIOSEQ_LOCUS5457 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6A5Q4V2, UniProt: P53851*PLUS #4: Protein | Mass: 45521.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) Gene: SUB2, GI526_G0000835, PACBIOSEQ_LOCUS934, PACBIOSEQ_LOCUS949, PACBIOSEQ_LOCUS951, PACBIOSEQ_LOCUS965 Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6A5Q316, UniProt: Q07478*PLUS #5: Protein | Mass: 30340.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) Gene: THP2, GI526_G0002950, PACBIOSEQ_LOCUS3229, PACBIOSEQ_LOCUS3284, PACBIOSEQ_LOCUS3351 Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6A5PZX4, UniProt: O13539*PLUS |
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-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 dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 862 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Saccharomyces cerevisiae 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 |
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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113076 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | |||||||||||||||||||||
Atomic model building | PDB-ID: 7APX Accession code: 7APX / Source name: PDB / Type: experimental model |