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)

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
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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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00571
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Nascimento, A.F.Z.

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.