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- EMDB-23527: Cryo-EM structure of the yeast THO-Sub2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-23527
TitleCryo-EM structure of the yeast THO-Sub2 complex
Map data
SampleTHO-Sub2:
Sub2 / THO / (Tex1) x 2 / (THO complex subunit ...) x 4 / ATP-dependent RNA helicase SUB2
Function / homology
Function and homology information


nucleoplasmic THO complex / THO complex part of transcription export complex / transcription export complex / Cdc73/Paf1 complex / positive regulation of transcription elongation from RNA polymerase I promoter / positive regulation of transcription by RNA polymerase I / mRNA 3'-end processing / chromatin silencing at telomere / stress granule assembly / molecular adaptor activity ...nucleoplasmic THO complex / THO complex part of transcription export complex / transcription export complex / Cdc73/Paf1 complex / positive regulation of transcription elongation from RNA polymerase I promoter / positive regulation of transcription by RNA polymerase I / mRNA 3'-end processing / chromatin silencing at telomere / stress granule assembly / molecular adaptor activity / transcription elongation from RNA polymerase II promoter / mRNA export from nucleus / spliceosomal complex / telomere maintenance / mRNA splicing, via spliceosome / transcription-coupled nucleotide-excision repair / mRNA processing / chromosome, telomeric region / nucleic acid binding / RNA helicase / DNA recombination / RNA helicase activity / mRNA binding / RNA binding / ATP binding / nucleus / cytoplasm
Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / THO complex subunit Thp2 / RNA helicase, DEAD-box type, Q motif / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex, subunit THOC1 / THO complex subunit 2, N-terminal domain / THO complex subunit 2 / Helicase, C-terminal ...Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / THO complex subunit Thp2 / RNA helicase, DEAD-box type, Q motif / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex, subunit THOC1 / THO complex subunit 2, N-terminal domain / THO complex subunit 2 / Helicase, C-terminal / THO complex subunit 7/Mft1 / DEAD/DEAH box helicase domain
THO complex subunit THP2 / THO complex subunit HPR1 / THO complex subunit MFT1 / THO complex subunit 2 / ATP-dependent RNA helicase SUB2
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Saccharomyces bayanus (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsXie Y / Ren Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133743 United States
CitationJournal: 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.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionFeb 23, 2021-
Header (metadata) releaseApr 14, 2021-
Map releaseApr 14, 2021-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7luv
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_23527.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 500 pix.
= 340.55 Å
0.68 Å/pix.
x 500 pix.
= 340.55 Å
0.68 Å/pix.
x 500 pix.
= 340.55 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6811 Å
Density
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.014631633 - 0.035607513
Average (Standard dev.)0.00015237037 (±0.0012308055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 340.55002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.68110.68110.6811
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z340.550340.550340.550
α/β/γ90.00090.00090.000
start NX/NY/NZ645365
NX/NY/NZ139143124
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0150.0360.000

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Supplemental data

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Additional map: Assembly composed of four copies of the THO-Sub2 complex.

Fileemd_23527_additional_1.map
AnnotationAssembly composed of four copies of the THO-Sub2 complex.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire THO-Sub2

EntireName: THO-Sub2 / Number of components: 10

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Component #1: protein, THO-Sub2

ProteinName: THO-Sub2 / Recombinant expression: No

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Component #2: protein, Sub2

ProteinName: Sub2 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: E. coli (E. coli)

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Component #3: protein, THO

ProteinName: THO / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #4: protein, Tex1

ProteinName: Tex1 / Recombinant expression: No
SourceSpecies: Saccharomyces bayanus (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #5: protein, THO complex subunit HPR1

ProteinName: THO complex subunit HPR1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 71.126195 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #6: protein, THO complex subunit THP2

ProteinName: THO complex subunit THP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.340264 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #7: protein, THO complex subunit 2

ProteinName: THO complex subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 138.881453 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #8: protein, THO complex subunit MFT1

ProteinName: THO complex subunit MFT1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.46748 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #9: protein, Tex1

ProteinName: Tex1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.248668 kDa
SourceSpecies: Saccharomyces bayanus (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #10: protein, ATP-dependent RNA helicase SUB2

ProteinName: ATP-dependent RNA helicase SUB2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.375859 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 30066
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL / Overall bvalue: 114.5
Output model

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