8KCA

Crystal structure of DDX53 helicase domain

• PDB DOI: https://doi.org/10.2210/pdb8KCA/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-06 Released: 2023-08-30 
• Deposition Author(s): Park, S., Yang, J.B., Jung, H.S., Kim, H.Y.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 

Literature

Structural insight into crystal structure of helicase domain of DDX53

Park, S., Yang, J.B., Park, Y.H., Kim, Y.K., Jeoung, D., Kim, H.Y., Jung, H.S.

(2023) Biochem Biophys Res Commun 677: 190-195

• DOI: https://doi.org/10.1016/j.bbrc.2023.08.022

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.11 kDa 
• Atom Count: 2,904 
• Modelled Residue Count: 346 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent RNA helicase DDX53	A, B	192	Homo sapiens	Mutation(s): 0  Gene Names: DDX53, CAGE EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q86TM3 (Homo sapiens) Explore Q86TM3  Go to UniProtKB:  Q86TM3
PHAROS:  Q86TM3 GTEx:  ENSG00000184735

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.866	α = 90
b = 106.494	β = 98.61
c = 41.943	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-30 
Deposition Author(s): Park, S., Yang, J.B., Jung, H.S., Kim, H.Y.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1A2C1009404
National Research Foundation (NRF, Korea)	Korea, Republic Of	2022R1F1A1060031

Revision History  

• Version 1.0: 2023-08-30
  Type: Initial release