6XWY | pdb_00006xwy

Highly pH-resistant long stokes-shift, red fluorescent protein mCRISPRed


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.232 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6XWY

This is version 1.3 of the entry. See complete history

Literature

Targeted In Situ Protein Diversification and Intra-organelle Validation in Mammalian Cells.

Erdogan, M.Fabritius, A.Basquin, J.Griesbeck, O.

(2020) Cell Chem Biol 27: 610-621.e5

  • DOI: https://doi.org/10.1016/j.chembiol.2020.02.004
  • Primary Citation Related Structures: 
    6XWY

  • PubMed Abstract: 

    Engineered proteins must be phenotypically selected for function in the appropriate physiological context. Here, we present a versatile approach that allows generating panels of mammalian cells that express diversified heterologous protein libraries in the cytosol or subcellular compartments under stable conditions and in a single-variant-per-cell manner. To this end we adapt CRISPR/Cas9 editing technology to diversify targeted stretches of a protein of interest in situ. We demonstrate the utility of the approach by in situ engineering and intra-lysosome specific selection of an extremely pH-resistant long Stokes shift red fluorescent protein variant. Tailoring properties to specific conditions of cellular sub-compartments or organelles of mammalian cells can be an important asset to optimize various proteins, protein-based tools, and biosensors for distinct functions.


  • Organizational Affiliation
    • Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany.

Macromolecule Content 

  • Total Structure Weight: 99.77 kDa 
  • Atom Count: 7,559 
  • Modeled Residue Count: 869 
  • Deposited Residue Count: 876 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Red fluorescent protein eqFP611
A, B, C, D
219Entacmaea quadricolorMutation(s): 1 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.232 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.02α = 90
b = 96.861β = 90
c = 232.922γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2020-06-03
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description