3IP2 | pdb_00003ip2

Crystal structure of red fluorescent protein Neptune at pH 7.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.202 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3IP2

This is version 2.0 of the entry. See complete history

Literature

Autofluorescent proteins with excitation in the optical window for intravital imaging in mammals.

Lin, M.Z.McKeown, M.R.Ng, H.L.Aguilera, T.A.Shaner, N.C.Campbell, R.E.Adams, S.R.Gross, L.A.Ma, W.Alber, T.Tsien, R.Y.

(2009) Chem Biol 16: 1169-1179

  • DOI: https://doi.org/10.1016/j.chembiol.2009.10.009
  • Primary Citation Related Structures: 
    3IP2

  • PubMed Abstract: 

    Fluorescent proteins have become valuable tools for biomedical research as protein tags, reporters of gene expression, biosensor components, and cell lineage tracers. However, applications of fluorescent proteins for deep tissue imaging in whole mammals have been constrained by the opacity of tissues to excitation light below 600 nm, because of absorbance by hemoglobin. Fluorescent proteins that excite efficiently in the "optical window" above 600 nm are therefore highly desirable. We report here the evolution of far-red fluorescent proteins with peak excitation at 600 nm or above. The brightest one of these, Neptune, performs well in imaging deep tissues in living mice. The crystal structure of Neptune reveals a novel mechanism for red-shifting involving the acquisition of a new hydrogen bond with the acylimine region of the chromophore.


  • Organizational Affiliation
    • Department of Pharmacology, University of California, San Diego, La Jolla, 92093, USA.

Macromolecule Content 

  • Total Structure Weight: 27.37 kDa 
  • Atom Count: 2,077 
  • Modeled Residue Count: 229 
  • Deposited Residue Count: 242 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neptune red fluorescent protein242Entacmaea quadricolorMutation(s): 0 
UniProt
Find proteins for Q8ISF8 (Entacmaea quadricolor)
Explore Q8ISF8 
Go to UniProtKB:  Q8ISF8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ISF8
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NRQ
Query on NRQ
A
L-PEPTIDE LINKINGC16 H17 N3 O4 SMET, TYR, GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.202 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.144α = 90
b = 92.144β = 90
c = 53.216γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-22
    Changes: Data collection
  • Version 2.0: 2026-03-18
    Changes: Polymer sequence, Structure summary