7AUG

Crystal structure of rsGCamP1.3 in the ON state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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

  • DOI: https://doi.org/10.1038/s41587-021-01100-5
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rsGCamP1.3420Aequorea victoriaMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth A]
DA [auth A]
EA [auth A]
FA [auth A]
GA [auth A]
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
J [auth A]
K [auth A]
L [auth A]
AA [auth A],
BA [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],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PIA
Query on PIA
A
L-PEPTIDE LINKINGC14 H15 N3 O4ALA, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.852α = 90
b = 121.852β = 90
c = 96.416γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySTI 656/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2021-12-22
    Changes: Database references
  • Version 1.2: 2022-04-27
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description