6MWQ

Single particle cryoEM structure of a DARPin-aldolase platform in complex with GFP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fusion of DARPin to Aldolase Enables Visualization of Small Protein by Cryo-EM.

Yao, Q.Weaver, S.J.Mock, J.Y.Jensen, G.J.

(2019) Structure 27: 1148

  • DOI: 10.1016/j.str.2019.04.003

  • PubMed Abstract: 
  • Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both e ...

    Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both eukaryotes and bacteria is still beyond the reach of cryo-EM. To overcome this problem, we implemented a platform strategy in which a small protein target was rigidly attached to a large, symmetric base via a selectable adapter. Of our seven designs, the best construct used a designed ankyrin repeat protein (DARPin) rigidly fused to tetrameric rabbit muscle aldolase through a helical linker. The DARPin retained its ability to bind its target: GFP. We solved the structure of this complex to 3.0 Å resolution overall, with 5-8 Å resolution in the GFP region. As flexibility in the DARPin position limited the overall resolution of the target, we describe strategies to rigidify this element.


    Related Citations: 
    • Fusion of DARPin to aldolase enables visualization of small protein by cryoEM
      Yao, Q.,Weaver, S.J.,Mock, J.Y.,Jensen, G.J.
      (2018) Biorxiv --: --


    Organizational Affiliation

    Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, 1200 E. California Boulevard, Pasadena, CA 91125, USA. Electronic address: jensen@caltech.edu.,Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DARPin, Muscle-type aldolase chimeric fusion
A, B, C, D
493Oryctolagus cuniculusMutation(s): 0 
Gene Names: ALDOA
EC: 4.1.2.13
Find proteins for P00883 (Oryctolagus cuniculus)
Go to Gene View: ALDOA
Go to UniProtKB:  P00883
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
G, J, I, H
226Aequorea victoriaMutation(s): 0 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-30 
  • Released Date: 2018-11-21 
  • Deposition Author(s): Weaver, S.J., Yao, Q.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP50 082545

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-05-29
    Type: Data collection, Database references
  • Version 1.2: 2019-07-17
    Type: Data collection, Database references