6RUL

Crystal structure of GFP-LAMA-F98 - a GFP enhancer nanobody with cpDHFR insertion and TMP and NADPH

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Chemogenetic Control of Nanobodies.

Farrants, H., Tarnawski, M., Muller, T.G., Otsuka, S., Hiblot, J., Koch, B., Kueblbeck, M., Krausslich, H.G., Ellenberg, J., Johnsson, K.

(2020) Nat Methods 17: 279-282

  • DOI: https://doi.org/10.1038/s41592-020-0746-7
  • Primary Citation of Related Structures:  
    6RUL, 6RUM

  • PubMed Abstract: 

    We introduce an engineered nanobody whose affinity to green fluorescent protein (GFP) can be switched on and off with small molecules. By controlling the cellular localization of GFP fusion proteins, the engineered nanobody allows interrogation of their roles in basic biological processes, an approach that should be applicable to numerous previously described GFP fusions. We also outline how the binding affinities of other nanobodies can be controlled by small molecules.

    • Organizational Affiliation: 

    Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion,Dihydrofolate reductase,GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion,Dihydrofolate reductase,Dihydrofolate reductase,GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion,Dihydrofolate reductase,GFP-LAMA-F98 a GFP enhancer nanobody with cpDHFR insertion279Lama glama, Escherichia coli K-12Mutation(s): 0 
EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12))
Explore P0ABQ4 
Go to UniProtKB:  P0ABQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABQ4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
TOP BindingDB:  6RUL Ki: min: 3, max: 8.3 (nM) from 2 assay(s)
IC50: min: 7, max: 1.20e+4 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.61α = 90
b = 86.61β = 90
c = 73.04γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary