3J9I

Thermoplasma acidophilum 20S proteasome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 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

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha
S, F, T, G, U, A, O, B, P, C, Q, D, R, E
224Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)Mutation(s): 0 
Gene Names: psmA
EC: 3.4.25.1
Find proteins for P25156 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Go to UniProtKB:  P25156
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta
Z, M, 1, N, 2, H, V, I, W, J, X, K, Y, L
203Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)Mutation(s): 0 
Gene Names: psmB
EC: 3.4.25.1
Find proteins for P28061 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Go to UniProtKB:  P28061
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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