6ZSM | pdb_00006zsm

Crystal structure of rsGCaMP double mutant Ile80His/Val116Ile in the ON state (non-illuminated)

PDB DOI: https://doi.org/10.2210/pdb6ZSM/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Aequorea victoria, Entacmaea quadricolor
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-07-16 Released: 2021-10-27
Deposition Author(s): Janowski, R., Fuenzalida-Werner, J.P., Mishra, K., Stiel, A.C., Niessing, D.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.198 (Depositor), 0.206 (DCC)
R-Value Work:
0.157 (Depositor), 0.169 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Genetically encoded photo-switchable molecular sensors for optoacoustic and super-resolution imaging.

Mishra, K., Fuenzalida-Werner, J.P., Pennacchietti, F., Janowski, R., Chmyrov, A., Huang, Y., Zakian, C., Klemm, U., Testa, I., Niessing, D., Ntziachristos, V., Stiel, A.C.

(2022) Nat Biotechnol 40: 598-605

PubMed: 34845372 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41587-021-01100-5
Primary Citation Related Structures:
6TV7, 6YA9, 6ZSM, 6ZSN, 7AUG

PubMed Abstract:
Reversibly photo-switchable proteins are essential for many super-resolution fluorescence microscopic and optoacoustic imaging methods. However, they have yet to be used as sensors that measure the distribution of specific analytes at the nanoscale or in the tissues of live animals. Here we constructed the prototype of a photo-switchable Ca ²⁺ sensor based on GCaMP5G that can be switched with 405/488-nm light and describe its molecular mechanisms at the structural level, including the importance of the interaction of the core barrel structure of the fluorescent protein with the Ca ²⁺ receptor moiety. We demonstrate super-resolution imaging of Ca ²⁺ concentration in cultured cells and optoacoustic Ca ²⁺ imaging in implanted tumor cells in mice under controlled Ca ²⁺ conditions. Finally, we show the generalizability of the concept by constructing examples of photo-switching maltose and dopamine sensors based on periplasmatic binding protein and G-protein-coupled receptor-based sensors.

Organizational Affiliation

Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Neuherberg, Germany.

Macromolecule Content

Total Structure Weight: 48.48 kDa
Atom Count: 3,729
Modeled Residue Count: 399
Deposited Residue Count: 418
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,Green fluorescent protein,Calmodulin	A	418	Aequorea victoria, Entacmaea quadricolor	Mutation(s): 0 Gene Names: GFP
UniProt
Find proteins for K4DIE3 (Entacmaea quadricolor) Explore K4DIE3 Go to UniProtKB: K4DIE3
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	K4DIE3 P42212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A]	U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]