5SUP

Structure of mRNA export factors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1.

Ren, Y.Schmiege, P.Blobel, G.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.20070
  • Primary Citation of Related Structures:  5SUQ

  • PubMed Abstract: 
  • mRNA is cotranscrptionally processed and packaged into messenger ribonucleoprotein particles (mRNPs) in the nucleus. Prior to export through the nuclear pore, mRNPs undergo several obligatory remodeling reactions. In yeast, one of these reactions inv ...

    mRNA is cotranscrptionally processed and packaged into messenger ribonucleoprotein particles (mRNPs) in the nucleus. Prior to export through the nuclear pore, mRNPs undergo several obligatory remodeling reactions. In yeast, one of these reactions involves loading of the mRNA-binding protein Yra1 by the DEAD-box ATPase Sub2 as assisted by the hetero-pentameric THO complex. To obtain molecular insights into reaction mechanisms, we determined crystal structures of two relevant complexes: a THO hetero-pentamer bound to Sub2 at 6.0 Å resolution; and Sub2 associated with an ATP analogue, RNA, and a C-terminal fragment of Yra1 (Yra1-C) at 2.6 Å resolution. We found that the 25 nm long THO clamps Sub2 in a half-open configuration; in contrast, when bound to the ATP analogue, RNA and Yra1-C, Sub2 assumes a closed conformation. Both THO and Yra1-C stimulated Sub2's intrinsic ATPase activity. We propose that THO surveys common landmarks in each nuclear mRNP to localize Sub2 for targeted loading of Yra1.


    Organizational Affiliation

    Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase SUB2
A, B, C
390Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SUB2
EC: 3.6.4.13
Find proteins for Q07478 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07478
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA annealing protein YRA1
G, H, I
32Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: YRA1
Find proteins for Q12159 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12159
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')D,E,F15synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A, B, C
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.346α = 90.00
b = 99.346β = 90.00
c = 247.469γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release