6NHT

Single particle reconstruction of the symmetric core an engineered protein scaffold

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: https://doi.org/10.1038/s41467-019-09836-0
  • Primary Citation of Related Structures:  
    6NHT, 6NHV

  • 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 designed protein scaffold to bind and symmetrically display 12 copies of a small 26 kDa protein, green fluorescent protein (GFP) ...

    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: 

    California NanoSystems Institute, Los Angeles, CA, 90095, USA. yeates@mbi.ucla.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DARP14 - Subunit A with DARPin
A, B, C, D, I
A, B, C, D, I, J, K, L, Q, R, S, T
319Pyrococcus horikoshii OT3Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DARP14 - Subunit B
E, F, G, H, M
E, F, G, H, M, N, O, P, U, V, W, X
131Pseudomonas aeruginosa PAO1Mutation(s): 8 
Gene Names: PA1966
UniProt
Find proteins for Q9I2D8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I2D8 
Go to UniProtKB:  Q9I2D8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I2D8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARCv.2.4.0

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence