3EWS

Human DEAD-box RNA-helicase DDX19 in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb3EWS/pdb

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


• Deposited: 2008-10-16 Released: 2008-11-04 
• Deposition Author(s): Lehtio, l., Karlberg, t., Andersson, j., Arrowsmith, c.h., Berglund, h., Bountra, c., Collins, r., Dahlgren, l.g., Edwards, a.m., Flodin, s., Flores, a., Graslund, s., Hammarstrom, m., Johansson, a., Johansson, i., Kotenyova, t., Moche, m., Nilsson, m.e., Nordlund, p., Nyman, t., Olesen, k., Persson, c., Sagemark, j., Thorsell, a.g., Tresaugues, l., Van den berg, s., Weigelt, j., Welin, m., Wikstrom, m., Wisniewska, m., Schueler, h., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.260 
• R-Value Work: 0.188 
• R-Value Observed: 0.192 

Literature

The DEXD/H-box RNA Helicase DDX19 Is Regulated by an {alpha}-Helical Switch.

Collins, R., Karlberg, T., Lehtio, L., Schutz, P., van den Berg, S., Dahlgren, L.G., Hammarstrom, M., Weigelt, J., Schuler, H.

(2009) J Biol Chem 284: 10296-10300

• PubMed: 19244245 
• DOI: https://doi.org/10.1074/jbc.C900018200
• Primary Citation of Related Structures:  
  3EWS, 3G0H


• PubMed Abstract: 
  

  DEXD/H-box RNA helicases couple ATP hydrolysis to RNA remodeling by an unknown mechanism. We used x-ray crystallography and biochemical analysis of the human DEXD/H-box protein DDX19 to investigate its regulatory mechanism. The crystal structures of DDX19, in its RNA-bound prehydrolysis and free posthydrolysis state, reveal an alpha-helix that inserts between the conserved domains of the free protein to negatively regulate ATPase activity. This finding was corroborated by biochemical data that confirm an autoregulatory function of the N-terminal region of the protein. This is the first study describing crystal structures of a DEXD/H-box protein in its open and closed cleft conformations.

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Organizational Affiliation: 

Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 101.85 kDa 
• Atom Count: 6,508 
• Modelled Residue Count: 821 
• Deposited Residue Count: 890 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX19B	A, B	445	Homo sapiens	Mutation(s): 0  Gene Names: DBP5, DDX19, DDX19B EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMR2 (Homo sapiens) Explore Q9UMR2  Go to UniProtKB:  Q9UMR2
PHAROS:  Q9UMR2 GTEx:  ENSG00000157349

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], D [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.260 
• R-Value Work: 0.188 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.58	α = 90
b = 47.61	β = 95.4
c = 124.69	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-04 
Deposition Author(s): Lehtio, l., Karlberg, t., Andersson, j., Arrowsmith, c.h., Berglund, h., Bountra, c., Collins, r., Dahlgren, l.g., Edwards, a.m., Flodin, s., Flores, a., Graslund, s., Hammarstrom, m., Johansson, a., Johansson, i., Kotenyova, t., Moche, m., Nilsson, m.e., Nordlund, p., Nyman, t., Olesen, k., Persson, c., Sagemark, j., Thorsell, a.g., Tresaugues, l., Van den berg, s., Weigelt, j., Welin, m., Wikstrom, m., Wisniewska, m., Schueler, h., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-11-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations