7QMO | pdb_00007qmo

Endothiapepsin in complex with compound TL00150 at room-temperature (temperature ramping down structure 16)

• PDB DOI: https://doi.org/10.2210/pdb7QMO/pdb

• Classification: HYDROLASE
• Organism(s): Cryphonectria parasitica
• Mutation(s): No 


• Deposited: 2021-12-20 Released: 2022-08-17 
• Deposition Author(s): Huang, C.Y., Aumonier, S., Wang, M.
• Funding Organization(s): Swiss National Science Foundation, H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography.

Huang, C.Y., Aumonier, S., Engilberge, S., Eris, D., Smith, K.M.L., Leonarski, F., Wojdyla, J.A., Beale, J.H., Buntschu, D., Pauluhn, A., Sharpe, M.E., Metz, A., Olieric, V., Wang, M.

(2022) Acta Crystallogr D Struct Biol 78: 964-974

• PubMed: 35916221 
• DOI: https://doi.org/10.1107/S205979832200612X
• Primary Citation Related Structures: 
  7QLT, 7QLU, 7QLV, 7QLW, 7QLX, 7QLY, 7QLZ, 7QM0, 7QM1, 7QM3, 7QM4, 7QM5, 7QM6, 7QM7, 7QM8, 7QM9, 7QMA, 7QMB, 7QMC, 7QMD, 7QME, 7QMF, 7QMG, 7QMH, 7QMI, 7QMJ, 7QMK, 7QML, 7QMM, 7QMN, 7QMO, 7QMP, 7QMQ, 7QMR, 7QMS, 7QMT, 7QMU, 7QMV, 7QMW, 7QMX, 7QMY, 7QMZ, 7QN0, 7QN1, 7QN2, 7QN3, 7QN4


• PubMed Abstract: 
  

  Continuous developments in cryogenic X-ray crystallography have provided most of our knowledge of 3D protein structures, which has recently been further augmented by revolutionary advances in cryoEM. However, a single structural conformation identified at cryogenic temperatures may introduce a fictitious structure as a result of cryogenic cooling artefacts, limiting the overview of inherent protein physiological dynamics, which play a critical role in the biological functions of proteins. Here, a room-temperature X-ray crystallographic method using temperature as a trigger to record movie-like structural snapshots has been developed. The method has been used to show how TL00150, a 175.15 Da fragment, undergoes binding-mode changes in endothiapepsin. A surprising fragment-binding discrepancy was observed between the cryo-cooled and physiological temperature structures, and multiple binding poses and their interplay with DMSO were captured. The observations here open up new promising prospects for structure determination and interpretation at physiological temperatures with implications for structure-based drug discovery.

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Organizational Affiliation: 
• Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, Villigen-PSI, 5232 Villigen, Switzerland.
Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 91, 4123 Allschwil, Switzerland.

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: 44.04 kDa 
• Atom Count: 2,631 
• Modeled Residue Count: 330 
• Deposited Residue Count: 419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothiapepsin	A	419	Cryphonectria parasitica	Mutation(s): 0  EC: 3.4.23.22
UniProt
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838  Go to UniProtKB:  P11838

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG5	C [auth A]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C8 H18 O4 YFNKIDBQEZZDLK-UHFFFAOYSA-N
U1H (Subject of Investigation/LOI)	B [auth A], G [auth A]	[4-(trifluoromethyl)phenyl]methanamine C8 H8 F3 N PRDBLLIPPDOICK-UHFFFAOYSA-N
DMS	D [auth A], E [auth A], F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.731	α = 90
b = 73.906	β = 109.72
c = 53.387	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-17 
Deposition Author(s): Huang, C.Y., Aumonier, S., Wang, M.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	European Union	182369
Swiss National Science Foundation	European Union	198290
H2020 Marie Curie Actions of the European Commission	European Union	884104

Revision History  

• Version 1.0: 2022-08-17
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary