5N9F | pdb_00005n9f

Crystal Structure of Drosophila DHX36 helicase in complex with ssDNA CpG_A

• PDB DOI: https://doi.org/10.2210/pdb5N9F/pdb
• NAKB: 5N9F

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


• Deposited: 2017-02-24 Released: 2018-03-21 
• Deposition Author(s): Chen, W.-F., Rety, S., Hai-Lei Guo, H.-L., Wu, W.-Q., Liu, N.-N., Liu, Q.-W., Dai, Y.-X., Xi, X.-G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 
  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structural and mechanistic insights into DHX36-mediated innate immunity and G-quadruplex unfolding

Chen, W.-F., Rety, S., Hai-Lei Guo, H.-L., Wu, W.-Q., Liu, N.-N., Liu, Q.-W., Dai, Y.-X., Xi, X.-G.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: SAXS

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: 223.08 kDa 
• Atom Count: 14,133 
• Modeled Residue Count: 1,734 
• Deposited Residue Count: 1,908 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CG9323, isoform A	A, B	944	Drosophila melanogaster	Mutation(s): 0  Gene Names: CG9323, Dmel_CG9323 EC: 3.6.1.3 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt
Find proteins for Q8SWT2 (Drosophila melanogaster) Explore Q8SWT2  Go to UniProtKB:  Q8SWT2

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*GP*AP*CP*GP*AP*TP*C)-3')	C, D	10	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 306.683	α = 90
b = 51.311	β = 115.55
c = 164.86	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Chen, W.-F., Rety, S., Hai-Lei Guo, H.-L., Wu, W.-Q., Liu, N.-N., Liu, Q.-W., Dai, Y.-X., Xi, X.-G.

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description