7ST4

Calcium-saturated jGCaMP8.410.80

PDB DOI: https://doi.org/10.2210/pdb7ST4/pdb

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

Deposited: 2021-11-11 Released: 2022-11-16
Deposition Author(s): Zhang, Y., Looger, L.L.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.197
R-Value Work: 0.175
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

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

Literature

Fast and sensitive GCaMP calcium indicators for imaging neural populations

Zhang, Y., Rozsa, M., Liang, Y., Bushey, D., Wei, Z., Zheng, J., Reep, D., Broussard, G.J., Tsang, A., Tsegaye, G., Narayan, S., Obara, C.J., Lim, J.X., Patel, R., Zhang, R., Ahrens, M.B., Turner, G.C., Wang, S.S.H., Korff, W.L., Schreiter, E.R., Svoboda, K., Hasseman, J.P., Kolb, I., Looger, L.L.

(2023) Nature 615: 884-891

DOI: https://doi.org/10.1038/s41586-023-05828-9

Macromolecule Content

Total Structure Weight: 47.94 kDa
Atom Count: 3,265
Modelled Residue Count: 386
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
jGCaMP8.410.80	A	420	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [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] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO Query on CRO	A	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.197
R-Value Work: 0.175
R-Value Observed: 0.176
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.597	α = 90
b = 120.597	β = 90
c = 97.876	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 1.1: 2023-08-02
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.