2I4I | pdb_00002i4i

Crystal Structure of human DEAD-box RNA helicase DDX3X

• PDB DOI: https://doi.org/10.2210/pdb2I4I/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-08-22 Released: 2006-09-05 
• Deposition Author(s): Hogbom, M., Karlberg, T., Arrowsmith, C., Berglund, H., Busam, R.D., Collins, R., Edwards, A., Ehn, M., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Johansson, I., Kotenyova, T., Magnusdottir, A., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Uppenberg, J., Van Den Berg, S., Wallden, K., Weigelt, J., Welin, M., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.218 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of Conserved Domains 1 and 2 of the Human DEAD-box Helicase DDX3X in Complex with the Mononucleotide AMP

Hogbom, M., Collins, R., van den Berg, S., Jenvert, R.-M., Karlberg, T., Kotenyova, T., Flores, A., Karlsson Hedestam, G.B., Holmberg Schiavone, L.H.

(2007) J Mol Biology 372: 150-159

• PubMed: 17631897 
• DOI: https://doi.org/10.1016/j.jmb.2007.06.050
• Primary Citation Related Structures: 
  2I4I


• PubMed Abstract: 
  

  DExD-box helicases are involved in all aspects of cellular RNA metabolism. Conserved domains 1 and 2 contain nine signature motifs that are responsible for nucleotide binding, RNA binding and ATP hydrolysis. The human DEAD-box helicase DDX3X has been associated with several different cellular processes, such as cell-growth control, mRNA transport and translation, and is suggested to be essential for the export of unspliced/partially spliced HIV mRNAs from the nucleus to the cytoplasm. Here, the crystal structure of conserved domains 1 and 2 of DDX3X, including a DDX3-specific insertion that is not generally found in human DExD-box helicases, is presented. The N-terminal domain 1 and the C-terminal domain 2 both display RecA-like folds comprising a central beta-sheet flanked by alpha-helices. Interestingly, the DDX3X-specific insertion forms a helical element that extends a highly positively charged sequence in a loop, thus increasing the RNA-binding surface of the protein. Surprisingly, although DDX3X was crystallized in the presence of a large excess of ADP or the slowly hydrolyzable ATP analogue ATPgammaS the contaminant AMP was seen in the structure. A fluorescent-based stability assay showed that the thermal stability of DDX3X was increased by the mononucleotide AMP but not by ADP or ATPgammaS, suggesting that DDX3X is stabilized by AMP and elucidating why AMP was found in the nucleotide-binding pocket.

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Organizational Affiliation: 
• Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.47 kDa 
• Atom Count: 3,465 
• Modeled Residue Count: 408 
• Deposited Residue Count: 417 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX3X	A	417	Homo sapiens	Mutation(s): 0  Gene Names: DDX3X EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O00571 (Homo sapiens) Explore O00571  Go to UniProtKB:  O00571
PHAROS:  O00571 GTEx:  ENSG00000215301

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.218 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.288	α = 90
b = 67.288	β = 90
c = 253.47	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DNA	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-05 
Deposition Author(s): Hogbom, M., Karlberg, T., Arrowsmith, C., Berglund, H., Busam, R.D., Collins, R., Edwards, A., Ehn, M., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Johansson, I., Kotenyova, T., Magnusdottir, A., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Uppenberg, J., Van Den Berg, S., Wallden, K., Weigelt, J., Welin, M., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-09-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description