5VNP | pdb_00005vnp

X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 
    0.229 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

AgHalo: A Facile Fluorogenic Sensor to Detect Drug-Induced Proteome Stress.

Liu, Y.Fares, M.Dunham, N.P.Gao, Z.Miao, K.Jiang, X.Bollinger, S.S.Boal, A.K.Zhang, X.

(2017) Angew Chem Int Ed Engl 56: 8672-8676

  • DOI: https://doi.org/10.1002/anie.201702417
  • Primary Citation Related Structures: 
    5VNP

  • PubMed Abstract: 

    Drug-induced proteome stress that involves protein aggregation may cause adverse effects and undermine the safety profile of a drug. Safety of drugs is regularly evaluated using cytotoxicity assays that measure cell death. However, these assays provide limited insights into the presence of proteome stress in live cells. A fluorogenic protein sensor is reported to detect drug-induced proteome stress prior to cell death. An aggregation prone Halo-tag mutant (AgHalo) was evolved to sense proteome stress through its aggregation. Detection of such conformational changes was enabled by a fluorogenic ligand that fluoresces upon AgHalo forming soluble aggregates. Using 5 common anticancer drugs, we exemplified detection of differential proteome stress before any cell death was observed. Thus, this sensor can be used to evaluate drug safety in a regime that the current cytotoxicity assays cannot cover and be generally applied to detect proteome stress induced by other toxins.


  • Organizational Affiliation
    • Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.

Macromolecule Content 

  • Total Structure Weight: 66.87 kDa 
  • Atom Count: 4,803 
  • Modeled Residue Count: 580 
  • Deposited Residue Count: 580 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Haloalkane dehalogenase
A, B
290Rhodococcus rhodochrousMutation(s): 0 
Gene Names: dhaA
EC: 3.8.1.5
UniProt
Find proteins for P0A3G2 (Rhodococcus rhodochrous)
Explore P0A3G2 
Go to UniProtKB:  P0A3G2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3G2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free:  0.229 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.272α = 90
b = 69.481β = 95.82
c = 88.95γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary