3FHC

Crystal structure of human Dbp5 in complex with Nup214


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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This is version 1.3 of the entry. See complete history


Literature

The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner

von Moeller, H.Basquin, C.Conti, E.

(2009) Nat Struct Mol Biol 16: 247-254

  • DOI: 10.1038/nsmb.1561
  • Primary Citation of Related Structures:  
    3FHT, 3FHC

  • PubMed Abstract: 
  • The DEAD-box protein DBP5 is essential for mRNA export in both yeast and humans. It binds RNA and is concentrated and locally activated at the cytoplasmic side of the nuclear pore complex. We have determined the crystal structures of human DBP5 bound to RNA and AMPPNP, and bound to the cytoplasmic nucleoporin NUP214 ...

    The DEAD-box protein DBP5 is essential for mRNA export in both yeast and humans. It binds RNA and is concentrated and locally activated at the cytoplasmic side of the nuclear pore complex. We have determined the crystal structures of human DBP5 bound to RNA and AMPPNP, and bound to the cytoplasmic nucleoporin NUP214. The structures reveal that binding of DBP5 to nucleic acid and to NUP214 is mutually exclusive. Using in vitro assays, we demonstrate that NUP214 decreases both the RNA binding and ATPase activities of DBP5. The interactions are mediated by conserved residues, implying a conserved recognition mechanism. These results suggest a framework for the consecutive steps leading to the release of mRNA at the final stages of nuclear export. More generally, they provide a paradigm for how binding of regulators can specifically inhibit DEAD-box proteins.


    Organizational Affiliation

    Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, D-82152 Martinsried, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup214 A405Homo sapiensMutation(s): 0 
Gene Names: Nup214 (Residues 1-405)NUP214CAINCANKIAA0023
Find proteins for P35658 (Homo sapiens)
Explore P35658 
Go to UniProtKB:  P35658
NIH Common Fund Data Resources
PHAROS:  P35658
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DDX19B B235Homo sapiensMutation(s): 0 
Gene Names: Dbp5 (Residues 68-302)DDX19BDBP5DDX19TDBP
EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.409α = 90
b = 134.707β = 90
c = 152.845γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-05
    Changes: Derived calculations
  • Version 1.3: 2019-11-06
    Changes: Advisory, Data collection