3IUY

Crystal structure of DDX53 DEAD-box domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comparative Structural Analysis of Human DEAD-Box RNA Helicases.

Schutz, P.Karlberg, T.van den Berg, S.Collins, R.Lehtio, L.Hogbom, M.Holmberg-Schiavone, L.Tempel, W.Park, H.W.Hammarstrom, M.Moche, M.Thorsell, A.G.Schuler, H.

(2010) Plos One 5: 12791-12791

  • DOI: 10.1371/journal.pone.0012791
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domain ...

    DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.


    Organizational Affiliation

    Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable ATP-dependent RNA helicase DDX53
A, B
228Homo sapiensMutation(s): 0 
Gene Names: DDX53 (CAGE)
EC: 3.6.4.13
Find proteins for Q86TM3 (Homo sapiens)
Go to Gene View: DDX53
Go to UniProtKB:  Q86TM3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.442α = 90.00
b = 61.251β = 96.36
c = 65.787γ = 90.00
Software Package:
Software NamePurpose
DNAdata collection
PDB_EXTRACTdata extraction
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-01-24
    Type: Data collection, Structure summary