6UV4

Crystal structure of the core domain of RNA helicase DDX17 with RNA pri-18a-oligo1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis.

Ngo, T.D.Partin, A.C.Nam, Y.

(2019) Cell Rep 29: 4024-4035.e5

  • DOI: 10.1016/j.celrep.2019.11.059
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DDX17, a DEAD-box ATPase, is a multifunctional helicase important for various RNA functions, including microRNA maturation. Key questions for DDX17 include how it recognizes target RNAs and influences their structures, as well as how its ATPase activ ...

    DDX17, a DEAD-box ATPase, is a multifunctional helicase important for various RNA functions, including microRNA maturation. Key questions for DDX17 include how it recognizes target RNAs and influences their structures, as well as how its ATPase activity may be regulated. Through crystal structures and biochemical assays, we show the ability of the core catalytic domains of DDX17 to recognize specific sequences in target RNAs. The RNA sequence preference of the catalytic core is critical for DDX17 to directly bind and remodel a specific region of primary microRNAs 3' to the mature sequence, and consequently enhance processing by Drosha. Furthermore, we identify an intramolecular interaction between the N-terminal tail and the DEAD domain of DDX17 to have an autoregulatory role in controlling the ATPase activity. Thus, we provide the molecular basis for how cognate RNA recognition and functional outcomes are linked for DDX17.


    Organizational Affiliation

    Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address: yunsun.nam@utsouthwestern.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable ATP-dependent RNA helicase DDX17
A
448Homo sapiensMutation(s): 0 
Gene Names: DDX17
EC: 3.6.4.13
Find proteins for Q92841 (Homo sapiens)
Go to Gene View: DDX17
Go to UniProtKB:  Q92841
Entity ID: 2
MoleculeChainsLengthOrganism
18a_oligo1C10Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 62.504α = 90.00
b = 62.504β = 90.00
c = 231.196γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-15
    Type: Structure summary