8THS | pdb_00008ths

Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA A69T

PDB DOI: https://doi.org/10.2210/pdb8THS/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-07-17 Released: 2023-11-29
Deposition Author(s): Henderson, J.N., Mills, J.H.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.188 (Depositor), 0.170 (DCC)
R-Value Work:
0.162 (Depositor), 0.172 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Capturing excited-state structural snapshots of evolutionary green-to-red photochromic fluorescent proteins.

Krueger, T.D., Henderson, J.N., Breen, I.L., Zhu, L., Wachter, R.M., Mills, J.H., Fang, C.

(2023) Front Chem 11: 1328081-1328081

PubMed: 38144887 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3389/fchem.2023.1328081
Primary Citation Related Structures:
8THS, 8UB6

PubMed Abstract:
Photochromic fluorescent proteins (FPs) have proved to be indispensable luminous probes for sophisticated and advanced bioimaging techniques. Among them, an interplay between photoswitching and photoconversion has only been observed in a limited subset of Kaede-like FPs that show potential for discovering the key mechanistic steps during green-to-red photoconversion. Various spectroscopic techniques including femtosecond stimulated Raman spectroscopy (FSRS), X-ray crystallography, and femtosecond transient absorption were employed on a set of five related FPs with varying photoconversion and photoswitching efficiencies. A 3-methyl-histidine chromophore derivative, incorporated through amber suppression using orthogonal aminoacyl tRNA synthetase/tRNA pairs, displays more dynamic photoswitching but greatly reduced photoconversion versus the least-evolved ancestor (LEA). Excitation-dependent measurements of the green anionic chromophore reveal that the varying photoswitching efficiencies arise from both the initial transient dynamics of the bright cis state and the final trans -like photoswitched off state, with an exocyclic bridge H-rocking motion playing an active role during the excited-state energy dissipation. This investigation establishes a close-knit feedback loop between spectroscopic characterization and protein engineering, which may be especially beneficial to develop more versatile FPs with targeted mutations and enhanced functionalities, such as photoconvertible FPs that also feature photoswitching properties.

Organizational Affiliation

Department of Chemistry, Oregon State University, Corvallis, OR, United States.

Macromolecule Content

Total Structure Weight: 106.59 kDa
Atom Count: 8,156
Modeled Residue Count: 873
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KAEDE-TYPE RED FLUORESCENT PROTEIN, LEA A69T	A, B, C, D	228	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B], J [auth B], L [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth B] Focus chain L [auth C]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth B], K [auth C], M [auth D]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]