6RUM | pdb_00006rum

Crystal structure of GFP-LAMA-G97 - a GFP enhancer nanobody with cpDHFR insertion and TMP and NADPH

• PDB DOI: https://doi.org/10.2210/pdb6RUM/pdb

• Classification: PROTEIN BINDING
• Organism(s): Lama glama, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-28 Released: 2020-02-12 
• Deposition Author(s): Farrants, H., Tarnawski, M., Mueller, T.G., Otsuka, S., Hiblot, J., Koch, B., Kueblbeck, M., Kraeusslich, H.-G., Ellenberg, J., Johnsson, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.228 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Models: experimental

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

• PubMed: 32066961 
• DOI: https://doi.org/10.1038/s41592-020-0746-7
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany.
Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany.
Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Max Perutz Labs, a joint venture of the University of Vienna and the Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany. [e-mail].
Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.43 kDa 
• Atom Count: 2,574 
• Modeled Residue Count: 276 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GFP-LAMA-G97 a GFP enhancer nanobody with cpDHFR insertion	A	279	Lama glama, Escherichia coli K-12	Mutation(s): 0  EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12)) Explore P0ABQ4  Go to UniProtKB:  P0ABQ4

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP (Subject of Investigation/LOI)	C [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
TOP (Subject of Investigation/LOI)	B [auth A]	TRIMETHOPRIM C14 H18 N4 O3 IEDVJHCEMCRBQM-UHFFFAOYSA-N
PG4	G [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
TOP	BindingDB:  6RUM	Ki: min: 3, max: 8.3 (nM) from 2 assay(s)
		IC50: min: 7, max: 1.20e+4 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.228 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.89	α = 90
b = 56.58	β = 94.91
c = 53.29	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): Farrants, H., Tarnawski, M., Mueller, T.G., Otsuka, S., Hiblot, J., Koch, B., Kueblbeck, M., Kraeusslich, H.-G., Ellenberg, J., Johnsson, K.

Revision History  

• 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