6GEL

The structure of TWITCH-2B

PDB DOI: https://doi.org/10.2210/pdb6GEL/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Aequorea victoria, Opsanus tau
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-04-26 Released: 2019-08-21
Deposition Author(s): Trigo Mourino, P., Paulat, M., Thestrup, T., Griesbeck, O., Griesinger, C., Becker, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.240
R-Value Work: 0.195
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Dynamic tuning of FRET in a green fluorescent protein biosensor.

Trigo-Mourino, P., Thestrup, T., Griesbeck, O., Griesinger, C., Becker, S.

(2019) Sci Adv 5: eaaw4988-eaaw4988

PubMed: 31457088 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.aaw4988
Primary Citation of Related Structures:
6GEL, 6GEZ

PubMed Abstract:
Förster resonance energy transfer (FRET) between mutants of green fluorescent protein is widely used to monitor protein-protein interactions and as a readout mode in fluorescent biosensors. Despite the fundamental importance of distance and molecular angles of fluorophores to each other, structural details on fluorescent protein FRET have been missing. Here, we report the high-resolution x-ray structure of the fluorescent proteins mCerulean3 and cpVenus within the biosensor Twitch-2B, as they undergo FRET and characterize the dynamics of this biosensor with $B$ 0 2 -dependent paramagnetic nuclear magnetic resonance at 900 MHz and 1.1 GHz. These structural data provide the unprecedented opportunity to calculate FRET from the x-ray structure and to compare it to experimental data in solution. We find that interdomain dynamics limits the FRET effect and show that a rigidification of the sensor further enhances FRET.

Organizational Affiliation

Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

Macromolecule Content

Total Structure Weight: 125.95 kDa
Atom Count: 8,685
Modelled Residue Count: 1,062
Deposited Residue Count: 1,104
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein	A, B	552	Aequorea victoria, Opsanus tau	Mutation(s): 2 Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Find proteins for W5IDB2 (Opsanus tau) Explore W5IDB2 Go to UniProtKB: W5IDB2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P42212W5IDB2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	F [auth A], G [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	E [auth A], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	H [auth A], I [auth A], N [auth B], O [auth B], P [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	C [auth A], D [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2 Query on CR2	A, B	L-PEPTIDE LINKING	C₁₃ H₁₃ N₃ O₄		GLY, TYR, GLY
CRF Query on CRF	A, B	L-PEPTIDE LINKING	C₁₇ H₁₈ N₄ O₄		THR, TRP, GLY