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- EMDB-11854: Structure of the human THO - UAP56 complex (Map C) -

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Basic information

Entry
Database: EMDB / ID: EMD-11854
TitleStructure of the human THO - UAP56 complex (Map C)
Map dataMap C sharpened (Map sharpening B-factor -160 A%u030A2)
Sample
  • Complex: THO - UAP56
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsPuehringer C / Hohmann U / Plaschka C
CitationJournal: Elife / Year: 2020
Title: Structure of the human core transcription-export complex reveals a hub for multivalent interactions.
Authors: Thomas Pühringer / Ulrich Hohmann / Laura Fin / Belén Pacheco-Fiallos / Ulla Schellhaas / Julius Brennecke / Clemens Plaschka /
Abstract: The export of mRNA from nucleus to cytoplasm requires the conserved and essential transcription and export (TREX) complex (THO-UAP56/DDX39B-ALYREF). TREX selectively binds mRNA maturation marks and ...The export of mRNA from nucleus to cytoplasm requires the conserved and essential transcription and export (TREX) complex (THO-UAP56/DDX39B-ALYREF). TREX selectively binds mRNA maturation marks and licenses mRNA for nuclear export by loading the export factor NXF1-NXT1. How TREX integrates these marks and achieves high selectivity for mature mRNA is poorly understood. Here, we report the cryo-electron microscopy structure of the human THO-UAP56/DDX39B complex at 3.3 Å resolution. The seven-subunit THO-UAP56/DDX39B complex multimerizes into a 28-subunit tetrameric assembly, suggesting that selective recognition of mature mRNA is facilitated by the simultaneous sensing of multiple, spatially distant mRNA regions and maturation marks. Two UAP56/DDX39B RNA helicases are juxtaposed at each end of the tetramer, which would allow one bivalent ALYREF protein to bridge adjacent helicases and regulate the TREX-mRNA interaction. Our structural and biochemical results suggest a conserved model for TREX complex function that depends on multivalent interactions between proteins and mRNA.
History
DepositionOct 17, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateDec 16, 2020-
Current statusDec 16, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0424
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0424
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7apk
  • Surface level: 0.0424
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11854.png

Downloads & links

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Map

FileDownload / File: emd_11854.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap C sharpened (Map sharpening B-factor -160 A%u030A2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 440 pix.
= 589.6 Å		1.34 Å/pix.
x 440 pix.
= 589.6 Å		1.34 Å/pix.
x 440 pix.
= 589.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0424 / Movie #1: 0.0424
Minimum - Maximum-0.054591272 - 0.14440963
Average (Standard dev.)-9.004037e-05 (±0.0029593643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 589.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z589.600589.600589.600
α/β/γ90.00090.00090.000
start NX/NY/NZ1081340
NX/NY/NZ13584349
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0550.144-0.000

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Supplemental data

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Additional map: Map C unsharpened

Fileemd_11854_additional_1.map
AnnotationMap C unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : THO - UAP56

EntireName: THO - UAP56
Components
  • Complex: THO - UAP56

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Supramolecule #1: THO - UAP56

SupramoleculeName: THO - UAP56 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant strain: Hi5
Molecular weightTheoretical: 1.836 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 26303 / Average exposure time: 3.8 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1570265
CTF correctionSoftware - Name: Warp (ver. 1.07)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 195098
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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