8JFY | pdb_00008jfy

Cryo-EM structure of RDGC/Ca2+-CaM complex

PDB DOI: https://doi.org/10.2210/pdb8JFY/pdb
EM Map EMD-36219: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Drosophila melanogaster
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-05-19 Released: 2024-11-27
Deposition Author(s): Liu, Z.M., Liu, W., Wu, C., Liu, J.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8JFY

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of RDGC/Ca2+-CaM complex

Liu, Z.M., Liu, W., Wu, C., Liu, J.

To be published.

Macromolecule Content

Total Structure Weight: 172.22 kDa
Atom Count: 11,870
Modeled Residue Count: 1,472
Deposited Residue Count: 1,496
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AT15141p	A, C [auth B]	149	Drosophila melanogaster	Mutation(s): 0 Gene Names: Cam-RB
UniProt
Find proteins for C6SUZ2 (Drosophila melanogaster) Explore C6SUZ2 Go to UniProtKB: C6SUZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6SUZ2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase rdgC	B [auth D], D [auth C]	599	Drosophila melanogaster	Mutation(s): 0 Gene Names: rdgC, CG44746 EC: 3.1.3.16
UniProt
Find proteins for P40421 (Drosophila melanogaster) Explore P40421 Go to UniProtKB: P40421
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40421
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain K [auth D] MOL2 format, chain T [auth C] MOL2 format, chain K [auth D] mmCIF format, chain T [auth C] mmCIF format, chain K [auth D]	K [auth D], T [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth D] Focus chain T [auth C] Interactions & Density Focus chain K [auth D] Focus chain T [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain I [auth D] MOL2 format, chain R [auth C] MOL2 format, chain I [auth D] mmCIF format, chain R [auth C] mmCIF format, chain I [auth D]	I [auth D], R [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain R [auth C] Interactions & Density Focus chain I [auth D] Focus chain R [auth C]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain J [auth D] MOL2 format, chain S [auth C] MOL2 format, chain J [auth D] mmCIF format, chain S [auth C] mmCIF format, chain J [auth D]	J [auth D], S [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Focus chain S [auth C] Interactions & Density Focus chain J [auth D] Focus chain S [auth C]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] L [auth D] E [auth A], F [auth A], G [auth A], H [auth A], L [auth D], M [auth D], N [auth B], O [auth B], P [auth B], Q [auth B], U [auth C], V [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-11-27
Type: Initial release
Version 1.1: 2025-06-18
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.