7LIU | pdb_00007liu

DDX3X bound to ATP analog and remodeled RNA:DNA hybrid

• PDB DOI: https://doi.org/10.2210/pdb7LIU/pdb
• NAKB: 7LIU

• Classification: RNA-BINDING PROTEIN/DNA,RNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-01-27 Released: 2022-08-24 
• Deposition Author(s): Enemark, E.J., Yu, S.
• Funding Organization(s): National Institute of General Medical Sciences (NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

DDX3X bound to ATP analog and remodeled RNA:DNA hybrid

Enemark, E.J., Yu, S.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 111.46 kDa 
• Atom Count: 7,658 
• Modeled Residue Count: 912 
• Deposited Residue Count: 928 
• Unique protein chains: 1
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX3X	A, B	450	Homo sapiens	Mutation(s): 0  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 ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'	C [auth X], D [auth Y]	14	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
08T (Subject of Investigation/LOI)	F [auth A], H [auth B]	[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium C10 H14 Be F3 N5 O10 P2 WOGYHYSOODLXII-KWIZKVQNSA-J
MG (Subject of Investigation/LOI)	E [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.476	α = 90
b = 114.476	β = 90
c = 281.793	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Enemark, E.J., Yu, S.

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Funding Organization	Location	Grant Number
National Institute of General Medical Sciences (NIGMS)	United States	NIGMS 1 R35 GM 136313-01

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description