4XTQ

Crystal structure of a mutant (C20S) of a near-infrared fluorescent protein BphP1-FP

• PDB DOI:  https://doi.org/10.2210/pdb4XTQ/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Rhodopseudomonas palustris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-23 Released: 2015-12-09 
• Deposition Author(s): Pletnev, S., Malashkevich, V.N.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), EU FP7 Program

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.208 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Molecular Basis of Spectral Diversity in Near-Infrared Phytochrome-Based Fluorescent Proteins.

Shcherbakova, D.M., Baloban, M., Pletnev, S., Malashkevich, V.N., Xiao, H., Dauter, Z., Verkhusha, V.V.

(2015) Chem Biol 22: 1540-1551

• PubMed: 26590639 
• DOI: https://doi.org/10.1016/j.chembiol.2015.10.007
• Primary Citation of Related Structures:  
  4XTQ


• PubMed Abstract: 
  

Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes (BphPs) are the probes of choice for deep-tissue imaging. Detection of several processes requires spectrally distinct NIR FPs. We developed an NIR FP, BphP1-FP, which has the most blue-shifted spectra and the highest fluorescence quantum yield among BphP-derived FPs. We found that these properties result from the binding of the biliverdin chromophore to a cysteine residue in the GAF domain, unlike natural BphPs and other BphP-based FPs. To elucidate the molecular basis of the spectral shift, we applied biochemical, structural and mass spectrometry analyses and revealed the formation of unique chromophore species. Mutagenesis of NIR FPs of different origins indicated that the mechanism of the spectral shift is general and can be used to design multicolor NIR FPs from other BphPs. We applied pairs of spectrally distinct point cysteine mutants to multicolor cell labeling and demonstrated that they perform well in model deep-tissue imaging.

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Organizational Affiliation: 

Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00029, Finland. Electronic address: [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: 36.67 kDa 
• Atom Count: 2,954 
• Modelled Residue Count: 303 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BphP1-FP/C20S	A	327	Rhodopseudomonas palustris	Mutation(s): 0
UniProt
Find proteins for B3Q7C0 (Rhodopseudomonas palustris (strain TIE-1)) Explore B3Q7C0  Go to UniProtKB:  B3Q7C0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BL8	B [auth A]	3-[2-[(Z)-[5-[(Z)-[(3R,4R)-3-ethenyl-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid C33 H36 N4 O6 WLDQKQLRZDEERT-IFTFHFPBSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.208 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.656	α = 90
b = 53.113	β = 90
c = 107.07	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-12-09 
Deposition Author(s): Pletnev, S., Malashkevich, V.N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA164468
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM073913
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM108579
EU FP7 Program	Finland	ERC-2013-ADG-340233
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	HHSN261200800001E

Revision History  

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 1.1: 2015-12-16
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence