8G3K

Cryo-EM imaging scaffold subunits A and B used to display KRAS G12C complex with GDP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 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

Cryo-EM structure determination of small therapeutic protein targets at 3 angstrom -resolution using a rigid imaging scaffold.

Castells-Graells, R.Meador, K.Arbing, M.A.Sawaya, M.R.Gee, M.Cascio, D.Gleave, E.Debreczeni, J.E.Breed, J.Leopold, K.Patel, A.Jahagirdar, D.Lyons, B.Subramaniam, S.Phillips, C.Yeates, T.O.

(2023) Proc Natl Acad Sci U S A 120: e2305494120-e2305494120

  • DOI: https://doi.org/10.1073/pnas.2305494120
  • Primary Citation of Related Structures:  
    8G3K, 8G42, 8G47, 8G4E, 8G4F, 8G4H

  • PubMed Abstract: 

    Cryoelectron microscopy (Cryo-EM) has enabled structural determination of proteins larger than about 50 kDa, including many intractable by any other method, but it has largely failed for smaller proteins. Here, we obtain structures of small proteins by binding them to a rigid molecular scaffold based on a designed protein cage, revealing atomic details at resolutions reaching 2.9 Å. We apply this system to the key cancer signaling protein KRAS (19 kDa in size), obtaining four structures of oncogenic mutational variants by cryo-EM. Importantly, a structure for the key G12C mutant bound to an inhibitor drug (AMG510) reveals significant conformational differences compared to prior data in the crystalline state. The findings highlight the promise of cryo-EM scaffolds for advancing the design of drug molecules against small therapeutic protein targets in cancer and other human diseases.


  • Organizational Affiliation

    Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cob_adeno_trans domain-containing protein178Thermoplasma acidophilumMutation(s): 0 
Gene Names: PH0671
UniProt
Find proteins for O58404 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58404 
Go to UniProtKB:  O58404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58404
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cryo-EM imaging scaffold subunit B with DARPin - RCG-33321synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20_4459

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM129854
Department of Energy (DOE, United States)United StatesDE-FC02-02ER63421

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references