6UV2

Crystal structure of the core domain of RNA helicase DDX17 with RNA pri-125a-oligo1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.celrep.2019.11.059
  • Primary Citation of Related Structures:  
    6UV0, 6UV1, 6UV2, 6UV3, 6UV4

  • 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 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.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX17448Homo sapiensMutation(s): 0 
Gene Names: DDX17
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q92841 (Homo sapiens)
Explore Q92841 
Go to UniProtKB:  Q92841
PHAROS:  Q92841
GTEx:  ENSG00000100201 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92841
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA 125a_oligo1B [auth C]10Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF (Subject of Investigation/LOI)
Query on BEF

Download Ideal Coordinates CCD File 
D [auth A]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.722α = 90
b = 112.722β = 90
c = 99.426γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Structure summary
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description