6FZN

SMURFP-Y56R mutant in complex with biliverdin

• PDB DOI: https://doi.org/10.2210/pdb6FZN/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-03-15 Released: 2018-10-17 
• Deposition Author(s): Janowski, R., Fuenzalida-Wernera, J.P., Mishra, K., Vetschera, P., Weidenfeld, I., Richter, K., Niessing, D., Ntziachristos, V., Stiel, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.263 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Literature

Crystal structure of a biliverdin-bound phycobiliprotein: Interdependence of oligomerization and chromophorylation.

Fuenzalida-Werner, J.P., Janowski, R., Mishra, K., Weidenfeld, I., Niessing, D., Ntziachristos, V., Stiel, A.C.

(2018) J Struct Biol 204: 519-522

• PubMed: 30287387 
• DOI: https://doi.org/10.1016/j.jsb.2018.09.013
• Primary Citation of Related Structures:  
  6FZN, 6FZO


• PubMed Abstract: 
  

  Small, ultra-red fluorescence protein (smURFP) introduces the non-native biliverdin (BV) chromophore to phycobiliproteins (PBPs), allowing them to be used as transgenic labels for in vivo mammalian imaging. Presently, no structural information exists for PBPs bound to the non-native BV chromophore, which limits the further development of smURFP and related proteins as imaging labels or indicators. Here we describe the first crystal structure of a PBP bound to BV. The structures of smURFP-Y56R with BV and smURFP-Y56F without BV reveal unique oligomerization interfaces different from those in wild-type PBPs bound to native chromophores. Our structures suggest that the oligomerization interface affects the BV binding site, creating a link between oligomerization and chromophorylation that we confirmed through site-directed mutagenesis and that may help guide efforts to improve the notorious chromophorylation of smURFP and other PBPs engineered to bind BV.

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Organizational Affiliation: 

Institute of Biological and Medical Imaging (IBMI), Helmholtz Zentrum München, Neuherberg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 32.05 kDa 
• Atom Count: 2,155 
• Modelled Residue Count: 265 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
smURFP	A, B	138	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9UY	C [auth A]	3-[5-[[(3~{R},4~{R})-3-ethenyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid C33 H38 N4 O6 IAVYOZQSRLDKLE-WOJBJXKFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.263 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.55	α = 90
b = 57.96	β = 105.04
c = 52.11	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Auto-Rickshaw	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Janowski, R., Fuenzalida-Wernera, J.P., Mishra, K., Vetschera, P., Weidenfeld, I., Richter, K., Niessing, D., Ntziachristos, V., Stiel, A.C.

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2018-12-26
  Changes: Data collection, Database references
• Version 1.2: 2019-02-20
  Changes: Data collection, Source and taxonomy