8D6N

Q108K:K40L:T53A:R58L:Q38F:Q4F mutant of hCRBPII bound to synthetic fluorophore CM1V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins.

Maity, S.Bingham, C.Sheng, W.Ehyaei, N.Chakraborty, D.Tahmasebi-Nick, S.Kimmel, T.E.Vasileiou, C.Geiger, J.H.Borhan, B.

(2023) Analyst 148: 1085-1092

  • DOI: https://doi.org/10.1039/d2an01395a
  • Primary Citation of Related Structures:  
    8D6H, 8D6L, 8D6N, 8DB2, 8DN1

  • PubMed Abstract: 

    Cysteine-based Michael addition is a widely employed strategy for covalent conjugation of proteins, peptides, and drugs. The covalent reaction is irreversible in most cases, leading to a lack of control over the process. Utilizing spectroscopic analyses along with X-ray crystallographic studies, we demonstrate Michael addition of an engineered cysteine residue in human Cellular Retinol Binding Protein II (hCRBPII) with a coumarin analog that creates a non-fluorescent complex. UV-illumination reverses the conjugation, yielding a fluorescent species, presumably through a retro -Michael process. This series of events can be repeated between a bound and non-bound form of the cysteine reversibly, resulting in the ON-OFF control of fluorescence. The details of the mechanism of photoswitching was illuminated by recapitulation of the process in light irradiated single crystals, confirming the mechanism at atomic resolution.


  • Organizational Affiliation

    Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA. babak@chemistry.msu.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinol-binding protein 2133Homo sapiensMutation(s): 6 
Gene Names: RBP2CRBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P50120 (Homo sapiens)
Explore P50120 
Go to UniProtKB:  P50120
PHAROS:  P50120
GTEx:  ENSG00000114113 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50120
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RH6
Query on RH6

Download Ideal Coordinates CCD File 
C [auth A](2E)-3-[7-(diethylamino)-2-oxo-2H-1-benzopyran-3-yl]prop-2-enal, bound form
C16 H19 N O2
YRIYSICZBXXPLJ-QPJJXVBHSA-N
MLA
Query on MLA

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
F [auth A]
H [auth A]
I [auth A]
J [auth A]
D [auth A],
F [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A],
E [auth A],
G [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.612α = 90
b = 67.106β = 90.108
c = 63.903γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2023-03-15
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary