+Open data
-Basic information
Entry | Database: PDB / ID: 7luv | ||||||
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Title | Cryo-EM structure of the yeast THO-Sub2 complex | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / nuclear mRNA export / DEAD-box ATPase / mRNP remodeling | ||||||
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) Saccharomyces bayanus (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Xie, Y. / Ren, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2021 Title: Cryo-EM structure of the yeast TREX complex and coordination with the SR-like protein Gbp2. Authors: Yihu Xie / Bradley P Clarke / Yong Joon Kim / Austin L Ivey / Pate S Hill / Yi Shi / Yi Ren / Abstract: The evolutionarily conserved TRanscript-EXport (TREX) complex plays central roles during mRNP (messenger ribonucleoprotein) maturation and export from the nucleus to the cytoplasm. In yeast, TREX is ...The evolutionarily conserved TRanscript-EXport (TREX) complex plays central roles during mRNP (messenger ribonucleoprotein) maturation and export from the nucleus to the cytoplasm. In yeast, TREX is composed of the THO sub-complex (Tho2, Hpr1, Tex1, Mft1, and Thp2), the DEAD box ATPase Sub2, and Yra1. Here we present a 3.7 Å cryo-EM structure of the yeast THO•Sub2 complex. The structure reveals the intimate assembly of THO revolving around its largest subunit Tho2. THO stabilizes a semi-open conformation of the Sub2 ATPase via interactions with Tho2. We show that THO interacts with the serine-arginine (SR)-like protein Gbp2 through both the RS domain and RRM domains of Gbp2. Cross-linking mass spectrometry analysis supports the extensive interactions between THO and Gbp2, further revealing that RRM domains of Gbp2 are in close proximity to the C-terminal domain of Tho2. We propose that THO serves as a landing pad to configure Gbp2 to facilitate its loading onto mRNP. | ||||||
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 | 7luv.cif.gz | 445 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7luv.ent.gz | 346.4 KB | Display | PDB format |
PDBx/mmJSON format | 7luv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7luv_validation.pdf.gz | 964 KB | Display | wwPDB validaton report |
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Full document | 7luv_full_validation.pdf.gz | 997.3 KB | Display | |
Data in XML | 7luv_validation.xml.gz | 64.7 KB | Display | |
Data in CIF | 7luv_validation.cif.gz | 100 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/7luv ftp://data.pdbj.org/pub/pdb/validation_reports/lu/7luv | HTTPS FTP |
-Related structure data
Related structure data | 23527MC 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: 71126.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HPR1, YDR138W, YD9302.14 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P17629 |
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#2: Protein | Mass: 30340.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: THP2, YHR167W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O13539 |
#3: Protein | Mass: 138881.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: THO2, LDB5, RLR1, ZRG13, YNL139C, N1209, N1835 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53552 |
#4: Protein | Mass: 29467.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MFT1, YML062C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P33441 |
-Protein , 2 types, 2 molecules EM
#5: Protein | Mass: 41248.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces bayanus (yeast) / Production host: Trichoplusia ni (cabbage looper) |
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#6: Protein | Mass: 50375.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SUB2, YDL084W / Production host: Escherichia coli (E. coli) / References: UniProt: Q07478, RNA helicase |
-Details
Sequence details | Certain segments of chains C and E were unidentifiable, and so they were modeled as poly-UNK. The ...Certain segments of chains C and E were unidentifiable, and so they were modeled as poly-UNK. The full sequence of chain C is: GAMGSMAEQT |
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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
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Source (recombinant) |
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Buffer solution | pH: 7 | ||||||||||||||||||||||||||||||
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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: PHENIX / Version: 1.11.1 / Category: model refinement | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30066 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 114.5 / Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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