5H1Y | pdb_00005h1y

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 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

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 Related Structures: 
  5H1Y

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
Baylor Research Institute, Baylor Scott and White Health, Dallas, TX, 75246, USA.
Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, 650500, China. [e-mail].
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA. [e-mail].

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 
• Modeled 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 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

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