Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.52 kDa 
• Atom Count: 4822 
• Residue Count: 605 
• Unique protein chains: 2

3FHC

Crystal structure of human Dbp5 in complex with Nup214

• DOI: 10.2210/pdb3FHC/pdb

• Classification: TRANSPORT PROTEIN/HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-12-09 Released: 2009-02-17 
• Deposition Author(s): von Moeller, H., Conti, E.

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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 

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

• PubMed: 19219046 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup214	A	405	Homo sapiens	Mutation(s): 0  Gene Names: Nup214 (Residues 1-405), NUP214, CAIN, CAN, KIAA0023
Find proteins for P35658 (Homo sapiens) Explore P35658  Go to UniProtKB:  P35658
NIH Common Fund Data Resources
PHAROS:  P35658 GTEx:  ENSG00000126883

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX19B	B	235	Homo sapiens	Mutation(s): 0  Gene Names: Dbp5 (Residues 68-302), DDX19B, DBP5, DDX19, TDBP 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 GTEx:  ENSG00000157349

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 = 117.409	α = 90
b = 134.707	β = 90
c = 152.845	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-12-09 
• Released Date: 2009-02-17 
Deposition Author(s): von Moeller, H., Conti, E.

Revision History 

• 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