5SUQ

Crystal structure of the THO-Sub2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.434 
  • R-Value Work: 0.436 
  • R-Value Observed: 0.436 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/10.7554/eLife.20070
  • Primary Citation of Related Structures:  
    5SUP, 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase SUB2
A, C
446Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUB2YDL084W
EC: 3.6.4.13
UniProt
Find proteins for Q07478 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07478 
Go to UniProtKB:  Q07478
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07478
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tex1
B, D
400Saccharomyces cerevisiaeMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tho2, Hpr1, Mft1, and Thp2E [auth M],
F [auth N]
2,300Saccharomyces cerevisiaeMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KEG
Query on KEG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth M]
K [auth M]
G [auth A],
H [auth A],
I [auth A],
J [auth M],
K [auth M],
L [auth M],
M [auth N],
N,
O [auth N],
P [auth N],
Q [auth N]
12-TUNGSTOPHOSPHATE
O40 P W12
WLQKSSFZMDTTCM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.434 
  • R-Value Work: 0.436 
  • R-Value Observed: 0.436 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.339α = 90
b = 319.534β = 100.96
c = 176.444γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Structure summary
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description