6DEJ

The structure of HcRed7, a brighter and red-shifted HcRed variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6279 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Monomerization of far-red fluorescent proteins.

Wannier, T.M.Gillespie, S.K.Hutchins, N.McIsaac, R.S.Wu, S.Y.Shen, Y.Campbell, R.E.Brown, K.S.Mayo, S.L.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E11294-E11301

  • DOI: 10.1073/pnas.1807449115

  • PubMed Abstract: 
  • <i>Anthozoa </i>-class red fluorescent proteins (RFPs) are frequently used as biological markers, with far-red (λ <sub>em </sub> ∼ 600-700 nm) emitting variants sought for whole-animal imaging because biological tissues are more permeable to light i ...

    Anthozoa -class red fluorescent proteins (RFPs) are frequently used as biological markers, with far-red (λ em ∼ 600-700 nm) emitting variants sought for whole-animal imaging because biological tissues are more permeable to light in this range. A barrier to the use of naturally occurring RFP variants as molecular markers is that all are tetrameric, which is not ideal for cell biological applications. Efforts to engineer monomeric RFPs have typically produced dimmer and blue-shifted variants because the chromophore is sensitive to small structural perturbations. In fact, despite much effort, only four native RFPs have been successfully monomerized, leaving the majority of RFP biodiversity untapped in biomarker development. Here we report the generation of monomeric variants of HcRed and mCardinal, both far-red dimers, and describe a comprehensive methodology for the monomerization of red-shifted oligomeric RFPs. Among the resultant variants is mKelly1 (emission maximum, λ em = 656 nm), which, along with the recently reported mGarnet2 [Matela G, et al. (2017) Chem Commun (Camb) 53:979-982], forms a class of bright, monomeric, far-red FPs.


    Organizational Affiliation

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125; timothy_wannier@hms.harvard.edu steve@mayo.caltech.edu.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125.,Department of Physics, University of Connecticut, Storrs, CT 06269.,Department of Marine Sciences, University of Connecticut, Groton, CT 06340.,Department of Chemical and Biomedical Engineering, University of Connecticut, Storrs, CT 06269.,Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.,Department of Chemistry, The University of Tokyo, 113-0033 Tokyo, Japan.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GFP-like non-fluorescent chromoprotein
A, B, C, D
237Heteractis crispaMutation(s): 8 
Find proteins for Q95W85 (Heteractis crispa)
Go to UniProtKB:  Q95W85
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
12P
Query on 12P

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Download CCD File 
B
DODECAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C24 H50 O13
WRZXKWFJEFFURH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRU
Query on CRU
A, B, C, D
L-PEPTIDE LINKINGC16 H15 N3 O6GLU, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6279 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.342α = 90.00
b = 122.057β = 108.75
c = 75.254γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement
Cootmodel building
Web-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United StatesR21EB018579

Revision History 

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-12-05
    Type: Data collection, Database references
  • Version 1.2: 2018-12-12
    Type: Data collection, Database references
  • Version 1.3: 2019-12-11
    Type: Author supporting evidence