5VIK

Crystal structure of monomeric near-infrared fluorescent protein miRFP703


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies.

Baloban, M.Shcherbakova, D.M.Pletnev, S.Pletnev, V.Z.Lagarias, J.C.Verkhusha, V.V.

(2017) Chem Sci 8: 4546-4557

  • DOI: 10.1039/c7sc00855d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Brighter near-infrared (NIR) fluorescent proteins (FPs) are required for multicolor microscopy and deep-tissue imaging. Here, we present structural and biochemical analyses of three monomeric, spectrally distinct phytochrome-based NIR FPs, termed miR ...

    Brighter near-infrared (NIR) fluorescent proteins (FPs) are required for multicolor microscopy and deep-tissue imaging. Here, we present structural and biochemical analyses of three monomeric, spectrally distinct phytochrome-based NIR FPs, termed miRFPs. The miRFPs are closely related and differ by only a few amino acids, which define their molecular brightness, brightness in mammalian cells, and spectral properties. We have identified the residues responsible for the spectral red-shift, revealed a new chromophore bound simultaneously to two cysteine residues in the PAS and GAF domains in blue-shifted NIR FPs, and uncovered the importance of amino acid residues in the N-terminus of NIR FPs for their molecular and cellular brightness. The novel chromophore covalently links the N-terminus of NIR FPs with their C-terminal GAF domain, forming a topologically closed knot in the structure, and also contributes to the increased brightness. Based on our studies, we suggest a strategy to develop spectrally distinct NIR FPs with enhanced brightness.


    Organizational Affiliation

    Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center , Albert Einstein College of Medicine , Bronx , New York 10461 , USA . Email: vladislav.verkhusha@einstein.yu.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
near-infrared fluorescent protein miRFP703
A
315Rhodopseudomonas palustris (strain TIE-1)Mutation(s): 0 
Find proteins for B3Q7C0 (Rhodopseudomonas palustris (strain TIE-1))
Go to UniProtKB:  B3Q7C0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLA
Query on BLA

Download SDF File 
Download CCD File 
A
BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.121 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.319α = 90.00
b = 52.821β = 92.53
c = 64.622γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-04-17 
  • Released Date: 2017-06-07 
  • Deposition Author(s): Pletnev, S.

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-10-04
    Type: Database references, Refinement description