6NHV

Single particle reconstruction of DARPin and its bound GFP on a symmetric scaffold


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A 3.8 angstrom resolution cryo-EM structure of a small protein bound to an imaging scaffold.

Liu, Y.Huynh, D.T.Yeates, T.O.

(2019) Nat Commun 10: 1864-1864

  • DOI: 10.1038/s41467-019-09836-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteins smaller than about 50 kDa are currently too small to be imaged at high resolution by cryo-electron microscopy (cryo-EM), leaving most protein molecules in the cell beyond the reach of this powerful structural technique. Here we use a designe ...

    Proteins smaller than about 50 kDa are currently too small to be imaged at high resolution by cryo-electron microscopy (cryo-EM), leaving most protein molecules in the cell beyond the reach of this powerful structural technique. Here we use a designed protein scaffold to bind and symmetrically display 12 copies of a small 26 kDa protein, green fluorescent protein (GFP). We show that the bound cargo protein is held rigidly enough to visualize it at a resolution of 3.8 Å by cryo-EM, where specific structural features of the protein are visible. The designed scaffold is modular and can be modified through modest changes in its amino acid sequence to bind and display diverse proteins for imaging, thus providing a general method to break through the lower size limitation in cryo-EM.


    Organizational Affiliation

    UCLA Department of Chemistry and Biochemistry, Los Angeles, CA, 90095, USA. yeates@mbi.ucla.edu.,UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, 90095, USA. yeates@mbi.ucla.edu.,UCLA Molecular Biology Institute, Los Angeles, CA, 90095, USA. yeates@mbi.ucla.edu.,UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, 90095, USA.,California NanoSystems Institute, Los Angeles, CA, 90095, USA. yeates@mbi.ucla.edu.,UCLA Department of Chemistry and Biochemistry, Los Angeles, CA, 90095, USA.,UCLA Molecular Biology Institute, Los Angeles, CA, 90095, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
superfolder GFP
A
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DARP14 - Subunit B
N, O, X
131Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 8 
Find proteins for Q9I2D8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I2D8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Subunit A-DARPin
R, S, T
319N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRO
Query on CRO
A
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (United States)United StatesDE-FC02-02ER63421
National Institutes of Health/National Human Genome Research InstituteUnited StatesS10RR23057
National Institutes of Health/National Human Genome Research InstituteUnited StatesS10OD018111
National Institutes of Health/National Human Genome Research InstituteUnited StatesU24GM11679
National Science Foundation (United States)United StatesDBI-1338135
National Science Foundation (United States)United StatesDMR-1548924

Revision History 

  • Version 1.0: 2019-05-08
    Type: Initial release