3J9I

Thermoplasma acidophilum 20S proteasome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.

Li, X.Mooney, P.Zheng, S.Booth, C.R.Braunfeld, M.B.Gubbens, S.Agard, D.A.Cheng, Y.

(2013) Nat Methods 10: 584-590

  • DOI: 10.1038/nmeth.2472
  • Primary Citation of Related Structures:  
    3J9I

  • PubMed Abstract: 
  • In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging ...

    In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron-counting detector, we confirmed that electron beam-induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to ∼3 Å). Using this approach, we determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency-key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples.


    Related Citations: 
    • Side-chain-directed model and map validation for 3D electron cryomicroscopy
      Barad, B.A., Echols, N., Wang, R.Y.-R., Cheng, Y., DiMaio, F., Adams, P.D., Fraser, J.S.
      () To be published --: --

    Organizational Affiliation

    The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco (UCSF), San Francisco, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha224Thermoplasma acidophilumMutation(s): 0 
Gene Names: psmATa1288
EC: 3.4.25.1
UniProt
Find proteins for P25156 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore P25156 
Go to UniProtKB:  P25156
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25156
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta203Thermoplasma acidophilumMutation(s): 0 
Gene Names: psmBTa0612
EC: 3.4.25.1
UniProt
Find proteins for P28061 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore P28061 
Go to UniProtKB:  P28061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28061
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection