9DHO | pdb_00009dho

Structure of proteinase K from energy-filtered MicroED data


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.09 Å
  • R-Value Free: 
    0.183 (Depositor) 
  • R-Value Work: 
    0.150 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Energy filtering enables macromolecular MicroED data at sub-atomic resolution.

Clabbers, M.T.B.Hattne, J.Martynowycz, M.W.Gonen, T.

(2025) Nat Commun 16: 2247-2247

  • DOI: https://doi.org/10.1038/s41467-025-57425-1
  • Primary Citation of Related Structures:  
    9DHO

  • PubMed Abstract: 

    High-resolution information is important for accurate structure modeling but is challenging to attain in macromolecular crystallography due to the rapid fading of diffracted intensities at increasing resolution. While direct electron detection essentially eliminates the read-out noise during MicroED data collection, other sources of noise remain and limit the measurement of faint high-resolution reflections. Inelastic scattering significantly contributes to noise, raising background levels and broadening diffraction peaks. We demonstrate a substantial improvement in signal-to-noise ratio by using energy filtering to remove inelastically scattered electrons. This strategy results in sub-atomic resolution MicroED data from proteinase K crystals, enabling the visualization of detailed structural features. Interestingly, reducing the noise further reveals diffuse scattering that may hold additional structural information. Our findings suggest that combining energy filtering and direct detection provides more accurate measurements at higher resolution, facilitating precise model refinement and improved insights into protein structure and function.


  • Organizational Affiliation
    • Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteinase K279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.09 Å
  • R-Value Free:  0.183 (Depositor) 
  • R-Value Work:  0.150 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.92α = 90
b = 66.92β = 90
c = 107.56γ = 90
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONphenix.refine1.21.1
MODEL REFINEMENTPHENIX1.21.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM136508
Department of Defense (DOD, United States)United StatesHDTRA1-21-1-0004
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Data collection, Database references, Structure summary