8IJU

ATP-dependent RNA helicase DDX39A (URH49delta41)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes.

Fujita, K.I.Ito, M.Irie, M.Harada, K.Fujiwara, N.Ikeda, Y.Yoshioka, H.Yamazaki, T.Kojima, M.Mikami, B.Mayeda, A.Masuda, S.

(2024) Nat Commun 15: 455-455

  • DOI: https://doi.org/10.1038/s41467-023-44217-8
  • Primary Citation of Related Structures:  
    8IJU

  • PubMed Abstract: 

    mRNA export is an essential pathway for the regulation of gene expression. In humans, closely related RNA helicases, UAP56 and URH49, shape selective mRNA export pathways through the formation of distinct complexes, known as apo-TREX and apo-AREX complexes, and their subsequent remodeling into similar ATP-bound complexes. Therefore, defining the unidentified components of the apo-AREX complex and elucidating the molecular mechanisms underlying the formation of distinct apo-complexes is key to understanding their functional divergence. In this study, we identify additional apo-AREX components physically and functionally associated with URH49. Furthermore, by comparing the structures of UAP56 and URH49 and performing an integrated analysis of their chimeric mutants, we exhibit unique structural features that would contribute to the formation of their respective complexes. This study provides insights into the specific structural and functional diversification of these two helicases that diverged from the common ancestral gene Sub2.


  • Organizational Affiliation

    Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan. kefujit@ncc.go.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DDX39A396Homo sapiensMutation(s): 0 
Gene Names: DDX39ADDX39
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O00148 (Homo sapiens)
Explore O00148 
Go to UniProtKB:  O00148
PHAROS:  O00148
GTEx:  ENSG00000123136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00148
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE (Subject of Investigation/LOI)
Query on PGE

Download Ideal Coordinates CCD File 
B [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.974α = 90
b = 96.606β = 95.51
c = 59.755γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan26292053
Japan Society for the Promotion of Science (JSPS)Japan17K19232
Japan Society for the Promotion of Science (JSPS)Japan19K22280
Japan Society for the Promotion of Science (JSPS)Japan19H02884
Japan Society for the Promotion of Science (JSPS)Japan21K19078
Japan Society for the Promotion of Science (JSPS)Japan22H02264
Japan Society for the Promotion of Science (JSPS)Japan19K15807

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release