Crystal structure of HaloTag complexed with VL1

Experimental Data Snapshot

  • Resolution: 1.49 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

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This is version 1.2 of the entry. See complete history


A chemical tool for blue light-inducible proximity photo-crosslinking in live cells.

Mishra, P.K.Kang, M.G.Lee, H.Kim, S.Choi, S.Sharma, N.Park, C.M.Ko, J.Lee, C.Seo, J.K.Rhee, H.W.

(2022) Chem Sci 13: 955-966

  • DOI: https://doi.org/10.1039/d1sc04871f
  • Primary Citation of Related Structures:  
    7WAM, 7WAN

  • PubMed Abstract: 

    We developed a proximity photo-crosslinking method ( Spotlight ) with a 4-azido- N -ethyl-1,8-naphthalimide (AzNP) moiety that can be converted to reactive aryl nitrene species using ambient blue light-emitting diode light. Using an AzNP-conjugated HaloTag ligand (VL1), blue light-induced photo-crosslinked products of various HaloTag-conjugated proteins of interest were detected in subcellular spaces in live cells. Chemical or heat stress-induced dynamic changes in the proteome were also detected, and photo-crosslinking in the mouse brain tissue was enabled. Using Spotlight , we further identified the host interactome of SARS-CoV-2 nucleocapsid (N) protein, which is essential for viral genome assembly. Mass analysis of the VL1-crosslinked product of N -HaloTag in HEK293T cells showed that RNA-binding proteins in stress granules were exclusively enriched in the cross-linked samples. These results tell that our method can reveal the interactome of protein of interest within a short distance in live cells.

  • Organizational Affiliation

    Department of Chemistry, Seoul National University Seoul 08826 Korea rheehw@snu.ac.kr.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Haloalkane dehalogenase299Rhodococcus sp. (in: high G+C Gram-positive bacteria)Mutation(s): 22 
Gene Names: dhaA
Find proteins for P0A3G3 (Rhodococcus sp)
Explore P0A3G3 
Go to UniProtKB:  P0A3G3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3G3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 8MH

Download Ideal Coordinates CCD File 
B [auth A]3-[6-(2-azanylhydrazinyl)-1,3-bis(oxidanylidene)benzo[de]isoquinolin-2-yl]-N-[2-(2-hexoxyethoxy)ethyl]propanamide
C25 H35 N5 O5
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.49 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.078α = 90
b = 63.078β = 90
c = 164.112γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description