6B4J

Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(AMPPNP) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and functional analysis of mRNA export regulation by the nuclear pore complex.

Lin, D.H.Correia, A.R.Cai, S.W.Huber, F.M.Jette, C.A.Hoelz, A.

(2018) Nat Commun 9: 2319-2319

  • DOI: 10.1038/s41467-018-04459-3
  • Primary Citation of Related Structures:  
    6B4E, 6B4G, 6B4F, 6B4I, 6B4H, 6B4K, 6B4J

  • PubMed Abstract: 
  • The nuclear pore complex (NPC) controls the passage of macromolecules between the nucleus and cytoplasm, but how the NPC directly participates in macromolecular transport remains poorly understood. In the final step of mRNA export, the DEAD-box helic ...

    The nuclear pore complex (NPC) controls the passage of macromolecules between the nucleus and cytoplasm, but how the NPC directly participates in macromolecular transport remains poorly understood. In the final step of mRNA export, the DEAD-box helicase DDX19 is activated by the nucleoporins Gle1, Nup214, and Nup42 to remove Nxf1•Nxt1 from mRNAs. Here, we report crystal structures of Gle1•Nup42 from three organisms that reveal an evolutionarily conserved binding mode. Biochemical reconstitution of the DDX19 ATPase cycle establishes that human DDX19 activation does not require IP 6 , unlike its fungal homologs, and that Gle1 stability affects DDX19 activation. Mutations linked to motor neuron diseases cause decreased Gle1 thermostability, implicating nucleoporin misfolding as a disease determinant. Crystal structures of human Gle1•Nup42•DDX19 reveal the structural rearrangements in DDX19 from an auto-inhibited to an RNA-binding competent state. Together, our results provide the foundation for further mechanistic analyses of mRNA export in humans.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA. hoelz@caltech.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin GLE1A, B317Homo sapiensMutation(s): 0 
Gene Names: GLE1GLE1L
Find proteins for Q53GS7 (Homo sapiens)
Explore Q53GS7 
Go to UniProtKB:  Q53GS7
NIH Common Fund Data Resources
PHAROS  Q53GS7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin like 2C, D49Homo sapiensMutation(s): 0 
Gene Names: NUPL2NUP42CG1
Find proteins for O15504 (Homo sapiens)
Explore O15504 
Go to UniProtKB:  O15504
NIH Common Fund Data Resources
PHAROS  O15504
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DDX19BE, F430Homo sapiensMutation(s): 0 
Gene Names: DDX19BDBP5DDX19TDBP
EC: 3.6.4.13
Find proteins for Q9UMR2 (Homo sapiens)
Explore Q9UMR2 
Go to UniProtKB:  Q9UMR2
NIH Common Fund Data Resources
PHAROS  Q9UMR2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download CCD File 
E, F
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
B, E, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.266 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.94α = 90
b = 73.56β = 95.07
c = 145.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-21
    Changes: Data collection