5H1Y

Crystal structure of the DDX41 DEAD domain in complex with SO42- and Mg2+

• PDB DOI: https://doi.org/10.2210/pdb5H1Y/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2016-10-13 Released: 2017-01-18 
• Deposition Author(s): Jiang, Y., Ouyang, S., Liu, Z.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.233 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Structural and functional analyses of human DDX41 DEAD domain

Jiang, Y., Zhu, Y., Qiu, W., Liu, Y.J., Cheng, G., Liu, Z.J., Ouyang, S.

(2017) Protein Cell 8: 72-76

• PubMed: 27928732 
• DOI: https://doi.org/10.1007/s13238-016-0351-9
• Primary Citation of Related Structures:  
  5H1Y

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63.68 kDa 
• Atom Count: 4,028 
• Modelled Residue Count: 487 
• Deposited Residue Count: 562 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent RNA helicase DDX41	A, B	281	Homo sapiens	Mutation(s): 0  Gene Names: DDX41, ABS EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJV9 (Homo sapiens) Explore Q9UJV9  Go to UniProtKB:  Q9UJV9
PHAROS:  Q9UJV9 GTEx:  ENSG00000183258

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.233 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.881	α = 90
b = 62.746	β = 94.32
c = 92.881	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
PHENIX	model building
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Jiang, Y., Ouyang, S., Liu, Z.J.

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Funding Organization	Location	Grant Number
	China	--

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-03-20
  Changes: Source and taxonomy