DEAD-box helicase DbpA bound to single stranded RNA and ADP/BeF3

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA.

Wurm, J.P.

(2023) RNA 29: 1339-1354

  • DOI: https://doi.org/10.1261/rna.079582.123
  • Primary Citation of Related Structures:  
    7PLI, 7PMM, 7PMQ

  • PubMed Abstract: 

    DEAD-box RNA helicases are implicated in most aspects of RNA biology, where these enzymes unwind short RNA duplexes in an ATP-dependent manner. During the central step of the unwinding cycle, the two domains of the helicase core form a distinct closed conformation that destabilizes the RNA duplex, which ultimately leads to duplex melting. Despite the importance of this step for the unwinding process no high-resolution structures of this state are available. Here, I used nuclear magnetic resonance spectroscopy and X-ray crystallography to determine structures of the DEAD-box helicase DbpA in the closed conformation, complexed with substrate duplexes and single-stranded unwinding product. These structures reveal that DbpA initiates duplex unwinding by interacting with up to three base-paired nucleotides and a 5' single-stranded RNA duplex overhang. These high-resolution snapshots, together with biochemical assays, rationalize the destabilization of the RNA duplex and are integrated into a conclusive model of the unwinding process.

  • Organizational Affiliation

    Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany jan-philip.wurm@ur.de.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DbpA459Escherichia coli K-12Mutation(s): 0 
Gene Names: dbpAb1343JW1337
Find proteins for P21693 (Escherichia coli (strain K12))
Explore P21693 
Go to UniProtKB:  P21693
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21693
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')24synthetic construct
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth F]
M [auth A]
P [auth B]
S [auth E]
V [auth J]
BA [auth F],
M [auth A],
P [auth B],
S [auth E],
V [auth J],
Y [auth I]
C10 H15 N5 O10 P2
Query on BEF

Download Ideal Coordinates CCD File 
CA [auth F]
N [auth A]
Q [auth B]
T [auth E]
W [auth J]
CA [auth F],
N [auth A],
Q [auth B],
T [auth E],
W [auth J],
Z [auth I]
Be F3
Query on MG

Download Ideal Coordinates CCD File 
AA [auth I]
DA [auth F]
O [auth A]
R [auth B]
U [auth E]
AA [auth I],
DA [auth F],
O [auth A],
R [auth B],
U [auth E],
X [auth J]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.643α = 97.157
b = 121.599β = 92.426
c = 122.417γ = 103.438
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2022-09-07 
  • Deposition Author(s): Wurm, J.P.

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyWU 988/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-01-31
    Changes: Refinement description