5VY4

Thermoplasma acidophilum 20S Proteasome using 200keV with image shift

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 1.5 of the entry. See complete history. 


Literature

Achieving better-than-3- angstrom resolution by single-particle cryo-EM at 200 keV.

Herzik, M.A., Wu, M., Lander, G.C.

(2017) Nat Methods 14: 1075-1078

  • DOI: https://doi.org/10.1038/nmeth.4461
  • Primary Citation of Related Structures:  
    5VY3, 5VY4, 5VY5

  • PubMed Abstract: 

    • Nearly all single-particle cryo-EM structures resolved to better than 4-Å resolution have been determined using 300-keV transmission electron microscopes (TEMs). We demonstrate that it is possible to obtain reconstructions of macromolecular complexes of different sizes to better than 3-Å resolution using a 200-keV TEM ...

    Nearly all single-particle cryo-EM structures resolved to better than 4-Å resolution have been determined using 300-keV transmission electron microscopes (TEMs). We demonstrate that it is possible to obtain reconstructions of macromolecular complexes of different sizes to better than 3-Å resolution using a 200-keV TEM. These structures are of sufficient quality to unambiguously assign amino acid rotameric conformations and identify ordered water molecules.

    Organizational Affiliation: 

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha
A,
AA [auth 0],
C,
E,
G,
I,
K,
M,
O,
Q,
S,
U,
W,
Y
224Thermoplasma acidophilumMutation(s): 0 
Gene Names: psmA, Ta1288
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 beta
B,
BA [auth 1],
D,
F,
H,
J,
L,
N,
P,
R,
T,
V,
X,
Z
203Thermoplasma acidophilumMutation(s): 0 
Gene Names: psmB, Ta0612
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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.11.1-2580
RECONSTRUCTIONRELION2.0

Structure Validation

View Full Validation Report



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

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United StatesDP2EB020402

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2017-10-25
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Database references
  • Version 1.4: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-12-11
    Changes: Author supporting evidence