Crystal structure of monomeric near-infrared fluorescent protein miRFP670

Experimental Data Snapshot

  • Resolution: 1.33 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1039/c7sc00855d
  • Primary Citation of Related Structures:  
    5VIK, 5VIQ, 5VIV

  • 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 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

    Macromolecular Crystallography Laboratory , National Cancer Institute , Leidos Biomedical Research Inc. , Basic Research Program , Argonne , Illinois 60439 , USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
monomeric near-infrared fluorescent protein miRFP670315Rhodopseudomonas palustrisMutation(s): 0 
Find proteins for A0A161I5N6 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore A0A161I5N6 
Go to UniProtKB:  A0A161I5N6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A161I5N6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 9V1

Download Ideal Coordinates CCD File 
C [auth A]3-[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]-5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]pro panoic acid
C33 H40 N4 O6
Query on 9UY

Download Ideal Coordinates CCD File 
B [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
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.33 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.539α = 90
b = 53.282β = 90
c = 107.397γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2017-06-21 
  • Deposition Author(s): Pletnev, S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary