9E2C | pdb_00009e2c

Crystal structure of DEAD-box RNA helicase DDX3X R326H mutant

• PDB DOI: https://doi.org/10.2210/pdb9E2C/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-10-22 Released: 2025-10-29 
• Deposition Author(s): Prado, P.F.V., Oliveira, J.F., Nascimento, A.F.Z.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

DDX3X is a chloride-sensitive DEAD-box RNA helicase

Rosa e Silva, I., Prado, P.F.V., Benevenutti, F.Z., Oliveira, R.R., Passos, A.R., Canateli, C., Messias, I.G., Trindade, D.M., Bortot, L.O., Sforca, M.L., Nascimento, A.F.Z., Mercaldi, G.F., Fonseca, M.C., de Oliveira, P.S.L., Carvalho, M., Smetana, J.H.C., Krepischi, A.C.V., Franchini, K.G., Oliveira, J.F.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 56.16 kDa 
• Atom Count: 3,460 
• Modeled Residue Count: 427 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of ATP-dependent RNA helicase DDX3X	A	498	Homo sapiens	Mutation(s): 1  Gene Names: DDX3X, DBX, DDX3 EC: 3.6.4.13
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
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.347	α = 90
b = 99.101	β = 90
c = 105.351	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Prado, P.F.V., Oliveira, J.F., Nascimento, A.F.Z.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2022/12010-0
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	407904/2023-9

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release