9DHO | pdb_00009dho

Structure of proteinase K from energy-filtered MicroED data

• PDB DOI: https://doi.org/10.2210/pdb9DHO/pdb
• EM Map EMD-46871: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Parengyodontium album
• Expression System: Parengyodontium album
• Mutation(s): No 


• Deposited: 2024-09-04 Released: 2025-03-19 
• Deposition Author(s): Clabbers, M.T.B., Hattne, J., Martynowycz, M.W., Gonen, T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Defense (DOD, United States), Howard Hughes Medical Institute (HHMI)

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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

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

• PubMed: 40050283 
• DOI: https://doi.org/10.1038/s41467-025-57425-1
• Primary Citation 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.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.
Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA.
Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA. [e-mail].
Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA. [e-mail].
Department of Physiology, University of California, Los Angeles, CA, 90095, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.1 kDa 
• Atom Count: 2,542 
• Modeled Residue Count: 279 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase K	A	279	Parengyodontium album	Mutation(s): 0  Gene Names: PROK EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873  Go to UniProtKB:  P06873

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 66.92	α = 90
b = 66.92	β = 90
c = 107.56	γ = 90

EM Software:

Task	Software Package	Version
RECONSTRUCTION	phenix.refine	1.21.1
MODEL REFINEMENT	PHENIX	1.21.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Clabbers, M.T.B., Hattne, J., Martynowycz, M.W., Gonen, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM136508
Department of Defense (DOD, United States)	United States	HDTRA1-21-1-0004
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

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