7WAM

Crystal structure of HaloTag complexed with VL1

• PDB DOI: https://doi.org/10.2210/pdb7WAM/pdb

• Classification: HYDROLASE
• Organism(s): Rhodococcus sp. (in: high G+C Gram-positive bacteria)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-12-14 Released: 2022-02-02 
• Deposition Author(s): Pratyush, M., Kang, M., Lee, H., Lee, C., Rhee, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.188 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Literature

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

• PubMed: 35211260 
• 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.

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Organizational Affiliation: 

Department of Chemistry, Seoul National University Seoul 08826 Korea [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: 34.24 kDa 
• Atom Count: 2,744 
• Modelled Residue Count: 294 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	299	Rhodococcus sp. (in: high G+C Gram-positive bacteria)	Mutation(s): 22  Gene Names: dhaA EC: 3.8.1.5
UniProt
Find proteins for P0A3G3 (Rhodococcus sp) Explore P0A3G3  Go to UniProtKB:  P0A3G3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8MH	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 SKQKTNKUYTUXKA-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 63.078	α = 90
b = 63.078	β = 90
c = 164.112	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Pratyush, M., Kang, M., Lee, H., Lee, C., Rhee, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• 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