7VNL

Sandercyanin mutant-F55A-Biliverdin complex

• PDB DOI: https://doi.org/10.2210/pdb7VNL/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Sander vitreus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-10-11 Released: 2022-05-25 
• Deposition Author(s): Yadav, K., Ghosh, S., Subramanian, R.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.225 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Phenylalanine stacking enhances the red fluorescence of biliverdin IX alpha on UV excitation in sandercyanin fluorescent protein.

Yadav, K., Ghosh, S., Barak, A., Schaefer, W., Subramanian, R.

(2022) FEBS Lett 596: 796-805

• PubMed: 35020202 
• DOI: https://doi.org/10.1002/1873-3468.14281
• Primary Citation of Related Structures:  
  7VNL, 7VNS


• PubMed Abstract: 
  

  Biliverdin IXα (BV) binds to several prokaryotic and eukaryotic proteins. How nature exploits the versatility of BV's properties is not fully understood. Unlike free BV, the Sandercyanin fluorescent protein bound to BV (SFP-BV) shows enhanced red fluorescence (675 nm) on excitation in the UV region (380 nm). Site-directed mutagenesis showed that the BV complex of two SFP variants, F55A and E79A, resulted in the loss of red fluorescence. Crystal structures of the complexes of these proteins with BV show the absence of stacking interactions of the F55 phenyl ring with BV. BV changes from ZZZssa conformation in the wild-type to ZZZsss conformation in the variants. In the nonfluorescent mutants, the lowest excited state is destabilized, resulting in nonradiative decay.

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Organizational Affiliation: 

Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 41.72 kDa 
• Atom Count: 2,909 
• Modelled Residue Count: 338 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sandercyanin Fluorescent Protein	A, B	183	Sander vitreus	Mutation(s): 1
UniProt
Find proteins for A0A1D5B367 (Sander vitreus) Explore A0A1D5B367  Go to UniProtKB:  A0A1D5B367

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLA (Subject of Investigation/LOI)	C [auth A], E [auth B]	BILIVERDINE IX ALPHA C33 H34 N4 O6 GWZYPXHJIZCRAJ-SRVCBVSDSA-N
PG4	D [auth A], F [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.225 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.388	α = 90
b = 158.388	β = 90
c = 81.073	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHENIX	phasing
DIALS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-25 
Deposition Author(s): Yadav, K., Ghosh, S., Subramanian, R.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR5801/INF/22/156/2012

Revision History  

• Version 1.0: 2022-05-25
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary