6B4F

Crystal structure of human Gle1 CTD-Nup42 GBM complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

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 helicase DDX19 is activated by the nucleoporins Gle1, Nup214, and Nup42 to remove Nxf1•Nxt1 from mRNAs ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin GLE1B [auth A], A [auth B]317Homo sapiensMutation(s): 0 
Gene Names: GLE1GLE1L
UniProt & NIH Common Fund Data Resources
Find proteins for Q53GS7 (Homo sapiens)
Explore Q53GS7 
Go to UniProtKB:  Q53GS7
PHAROS:  Q53GS7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin like 2C, D50Homo sapiensMutation(s): 0 
Gene Names: NUPL2NUP42CG1
UniProt & NIH Common Fund Data Resources
Find proteins for O15504 (Homo sapiens)
Explore O15504 
Go to UniProtKB:  O15504
PHAROS:  O15504
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A], H [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.66α = 90
b = 69.71β = 90.66
c = 93.57γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5 T32 GM07616
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM117360
Howard Hughes Medical Institute (HHMI)United States--
Heritage Medical Research InstituteUnited States--
Sidney Kimmel Foundation for Cancer ResearchUnited States--
Camille & Henry Dreyfus FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence