8UGW | pdb_00008ugw

Computational design of highly signaling active membrane receptors through de novo solvent-mediated allosteric networks


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 
    0.330 (Depositor), 0.328 (DCC) 
  • R-Value Work: 
    0.300 (Depositor), 0.307 (DCC) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks.

Chen, K.M.Lai, J.K.Rudden, L.S.P.Wang, J.Russell, A.M.Conners, K.Rutter, M.E.Condon, B.Tung, F.Kodandapani, L.Chau, B.Zhao, X.Benach, J.Baker, K.Hembre, E.J.Barth, P.

(2025) Nat Chem 17: 429-438

  • DOI: https://doi.org/10.1038/s41557-024-01719-2
  • Primary Citation of Related Structures:  
    8UGW

  • PubMed Abstract: 

    Protein catalysis and allostery require the atomic-level orchestration and motion of residues and ligand, solvent and protein effector molecules. However, the ability to design protein activity through precise protein-solvent cooperative interactions has not yet been demonstrated. Here we report the design of 14 membrane receptors that catalyse G protein nucleotide exchange through diverse engineered allosteric pathways mediated by cooperative networks of intraprotein, protein-ligand and -solvent molecule interactions. Consistent with predictions, the designed protein activities correlated well with the level of plasticity of the networks at flexible transmembrane helical interfaces. Several designs displayed considerably enhanced thermostability and activity compared with related natural receptors. The most stable and active variant crystallized in an unforeseen signalling-active conformation, in excellent agreement with the design models. The allosteric network topologies of the best designs bear limited similarity to those of natural receptors and reveal an allosteric interaction space larger than previously inferred from natural proteins. The approach should prove useful for engineering proteins with novel complex protein binding, catalytic and signalling activities.


  • Organizational Affiliation
    • Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endolysin,Adenosine receptor A2a472Tequatrovirus T4Homo sapiens
This entity is chimeric
Mutation(s): 0 
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P29274 (Homo sapiens)
Explore P29274 
Go to UniProtKB:  P29274
PHAROS:  P29274
GTEx:  ENSG00000128271 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P29274
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGI (Subject of Investigation/LOI)
Query on NGI

Download Ideal Coordinates CCD File 
B [auth A]2-[P-(2-CARBOXYETHYL)PHENYLETHYL-AMINO]-5'-N-ETHYLCARBOXAMIDO ADENOSINE
C23 H29 N7 O6
PAOANWZGLPPROA-RQXXJAGISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free:  0.330 (Depositor), 0.328 (DCC) 
  • R-Value Work:  0.300 (Depositor), 0.307 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.179α = 90
b = 73.668β = 90
c = 149.847γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Database references
  • Version 1.2: 2025-03-12
    Changes: Database references