5CV3

C. remanei PGL-1 Dimerization Domain - Hg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17015 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

PGL germ granule assembly protein is a base-specific, single-stranded RNase.

Aoki, S.T.Kershner, A.M.Bingman, C.A.Wickens, M.Kimble, J.

(2016) Proc.Natl.Acad.Sci.USA 113: 1279-1284

  • DOI: 10.1073/pnas.1524400113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cellular RNA-protein (RNP) granules are ubiquitous and have fundamental roles in biology and RNA metabolism, but the molecular basis of their structure, assembly, and function is poorly understood. Using nematode "P-granules" as a paradigm, we focus ...

    Cellular RNA-protein (RNP) granules are ubiquitous and have fundamental roles in biology and RNA metabolism, but the molecular basis of their structure, assembly, and function is poorly understood. Using nematode "P-granules" as a paradigm, we focus on the PGL granule scaffold protein to gain molecular insights into RNP granule structure and assembly. We first identify a PGL dimerization domain (DD) and determine its crystal structure. PGL-1 DD has a novel 13 α-helix fold that creates a positively charged channel as a homodimer. We investigate its capacity to bind RNA and discover unexpectedly that PGL-1 DD is a guanosine-specific, single-stranded endonuclease. Discovery of the PGL homodimer, together with previous results, suggests a model in which the PGL DD dimer forms a fundamental building block for P-granule assembly. Discovery of the PGL RNase activity expands the role of RNP granule assembly proteins to include enzymatic activity in addition to their job as structural scaffolds.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
A
248Caenorhabditis remaneiMutation(s): 0 
Gene Names: pgl-1
EC: 3.1.27.3
Find proteins for E3M3V1 (Caenorhabditis remanei)
Go to UniProtKB:  E3M3V1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EMC
Query on EMC

Download SDF File 
Download CCD File 
A
ETHYL MERCURY ION
C2 H5 Hg
MJOUBOKSWBMNGQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17015 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.219 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.312α = 90.00
b = 87.312β = 90.00
c = 45.059γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
Cootmodel building
SCALEPACKdata scaling
SHARPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human DevelopmentUnited States5F32HD071692

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-10
    Type: Database references
  • Version 1.2: 2016-04-06
    Type: Source and taxonomy
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence, Derived calculations, Refinement description