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- PDB-8jfy: Cryo-EM structure of RDGC/Ca2+-CaM complex -

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Basic information

Entry
Database: PDB / ID: 8jfy
TitleCryo-EM structure of RDGC/Ca2+-CaM complex
Components
  • AT15141p
  • Serine/threonine-protein phosphatase rdgC
KeywordsHYDROLASE / Phosphatase / metal binding.
Function / homology
Function and homology information


detection of stimulus involved in sensory perception / negative regulation of opsin-mediated signaling pathway / calcium-dependent protein serine/threonine phosphatase activity / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / myosin phosphatase activity ...detection of stimulus involved in sensory perception / negative regulation of opsin-mediated signaling pathway / calcium-dependent protein serine/threonine phosphatase activity / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / myosin phosphatase activity / thermotaxis / calmodulin-dependent protein phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phototransduction / visual perception / calcium-mediated signaling / manganese ion binding / calmodulin binding / iron ion binding / calcium ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein phosphatase with EF-hands / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / IQ motif profile. ...Serine/threonine-protein phosphatase with EF-hands / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / IQ motif profile. / Metallo-dependent phosphatase-like / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
: / PHOSPHATE ION / AT15141p / Serine/threonine-protein phosphatase rdgC
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsLiu, Z.M. / Liu, W. / Wu, C. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of RDGC/Ca2+-CaM complex
Authors: Liu, Z.M. / Liu, W. / Wu, C. / Liu, J.
History
DepositionMay 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 27, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AT15141p
D: Serine/threonine-protein phosphatase rdgC
B: AT15141p
C: Serine/threonine-protein phosphatase rdgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,22122
Polymers171,3084
Non-polymers91318
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 4 molecules ABDC

#1: Protein AT15141p / Calmodulin / isoform C


Mass: 16825.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Cam-RB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C6SUZ2
#2: Protein Serine/threonine-protein phosphatase rdgC / Retinal degeneration C protein


Mass: 68828.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: rdgC, CG44746 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P40421, protein-serine/threonine phosphatase

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Non-polymers , 4 types, 18 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of RDGC/Ca2+-CaM complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56344 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026128
ELECTRON MICROSCOPYf_angle_d0.5098264
ELECTRON MICROSCOPYf_dihedral_angle_d3.501816
ELECTRON MICROSCOPYf_chiral_restr0.039896
ELECTRON MICROSCOPYf_plane_restr0.0031088

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