+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23527 | |||||||||
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Title | Cryo-EM structure of the yeast THO-Sub2 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | nuclear mRNA export / DEAD-box ATPase / mRNP remodeling / RNA BINDING PROTEIN | |||||||||
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 / DNA recombination / nucleic acid binding / chromosome, telomeric region / 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 | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Xie Y / Ren Y | |||||||||
Funding support | United States, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23527.map.gz | 325.5 MB | EMDB map data format | |
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Header (meta data) | emd-23527-v30.xml emd-23527.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
Images | emd_23527.png | 48.4 KB | ||
Filedesc metadata | emd-23527.cif.gz | 7.5 KB | ||
Others | emd_23527_additional_1.map.gz | 326.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23527 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23527 | HTTPS FTP |
-Validation report
Summary document | emd_23527_validation.pdf.gz | 560.9 KB | Display | EMDB validaton report |
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Full document | emd_23527_full_validation.pdf.gz | 560.5 KB | Display | |
Data in XML | emd_23527_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | emd_23527_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23527 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23527 | HTTPS FTP |
-Related structure data
Related structure data | 7luvMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_23527.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.6811 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Assembly composed of four copies of the THO-Sub2 complex.
File | emd_23527_additional_1.map | ||||||||||||
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Annotation | Assembly composed of four copies of the THO-Sub2 complex. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : THO-Sub2
+Supramolecule #1: THO-Sub2
+Supramolecule #2: Sub2
+Supramolecule #3: THO
+Supramolecule #4: Tex1
+Macromolecule #1: THO complex subunit HPR1
+Macromolecule #2: THO complex subunit THP2
+Macromolecule #3: THO complex subunit 2
+Macromolecule #4: THO complex subunit MFT1
+Macromolecule #5: Tex1
+Macromolecule #6: ATP-dependent RNA helicase SUB2
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30066 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 114.5 |
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Output model | PDB-7luv: |