4ON9

DECH box helicase domain

• PDB DOI: https://doi.org/10.2210/pdb4ON9/pdb

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


• Deposited: 2014-01-28 Released: 2014-07-02 
• Deposition Author(s): Deimling, T., Witte, G., Hopfner, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal and solution structure of the human RIG-I SF2 domain

Deimling, T., Cui, S., Lammens, K., Hopfner, K.P., Witte, G.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 1027-1031

• PubMed: 25084375 
• DOI: https://doi.org/10.1107/S2053230X14012230
• Primary Citation of Related Structures:  
  4ON9


• PubMed Abstract: 
  

  RIG-I is a pathogen-recognition receptor that recognizes viral 5'-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. Here, the crystal structure of the human RIG-I superfamily 2 ATPase domain crystallized in an unusually elongated and open conformation is reported. The elongated structure is probably induced in part by crystal packing, but nevertheless indicates that the domain is intrinsically very flexible. This flexibility might allow substantial structural changes upon substrate binding and oligomerization.

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Organizational Affiliation: 

Gene Center and Department of Biochemistry, Ludwig-Maximilians University Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.

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.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 132.63 kDa 
• Atom Count: 8,183 
• Modelled Residue Count: 1,009 
• Deposited Residue Count: 1,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent RNA helicase DDX58	A, B	580	Homo sapiens	Mutation(s): 0  Gene Names: DDX58 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O95786 (Homo sapiens) Explore O95786  Go to UniProtKB:  O95786
PHAROS:  O95786 GTEx:  ENSG00000107201

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.91	α = 90
b = 112.99	β = 90
c = 124.26	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Deimling, T., Witte, G., Hopfner, K.P.

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2014-08-06
  Changes: Database references
• Version 1.2: 2015-03-11
  Changes: Database references
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description