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- PDB-8duj: Global map in C1 of RyR1 particles in complex with ImperaCalcin -

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Basic information

Entry
Database: PDB / ID: 8duj
TitleGlobal map in C1 of RyR1 particles in complex with ImperaCalcin
Components
  • Calmodulin-1
  • Imperacalcin
  • Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ryanodine receptor 1
KeywordsMEMBRANE PROTEIN / ryanodine receptor / ion channel / snake toxin / calcin / complex / toxin
Function / homology
Function and homology information


ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / insulin secretion involved in cellular response to glucose stimulus / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity ...ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / insulin secretion involved in cellular response to glucose stimulus / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Calmodulin induced events / response to redox state / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / ossification involved in bone maturation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / 'de novo' protein folding / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / negative regulation of heart rate / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / skin development / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / FK506 binding / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / organelle membrane / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / cellular response to caffeine / RHO GTPases activate PAKs / intracellularly gated calcium channel activity / Ion transport by P-type ATPases / outflow tract morphogenesis / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / smooth muscle contraction / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / toxic substance binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / T cell proliferation / smooth endoplasmic reticulum / striated muscle contraction / voltage-gated calcium channel activity / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / presynaptic cytosol / Activation of AMPK downstream of NMDARs / skeletal muscle fiber development / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / release of sequestered calcium ion into cytosol / voltage-gated potassium channel complex / calcium channel complex / substantia nigra development / FCERI mediated Ca+2 mobilization / sarcoplasmic reticulum membrane / Ras activation upon Ca2+ influx through NMDA receptor / muscle contraction / regulation of heart rate / FCGR3A-mediated IL10 synthesis / calyx of Held / cellular response to calcium ion / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein maturation / adenylate cyclase activator activity / sarcoplasmic reticulum / sarcomere
Similarity search - Function
Scorpion calcine / Scorpion calcine family / Scorpion calcine family signature. / Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 ...Scorpion calcine / Scorpion calcine family / Scorpion calcine family signature. / Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / : / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / : / 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 / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CAFFEINE / Calmodulin-1 / Ryanodine receptor 1 / Imperacalcin / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
Pandinus imperator (emperor scorpion)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHaji-Ghassemi, O. / Van Petegm, F.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-159601 Canada
Canadian Institutes of Health Research (CIHR)MFE-381863 Canada
CitationJournal: Sci Adv / Year: 2023
Title: Cryo-EM analysis of scorpion toxin binding to Ryanodine Receptors reveals subconductance that is abolished by PKA phosphorylation.
Authors: Omid Haji-Ghassemi / Yu Seby Chen / Kellie Woll / Georgina B Gurrola / Carmen R Valdivia / Wenxuan Cai / Songhua Li / Hector H Valdivia / Filip Van Petegem /
Abstract: Calcins are peptides from scorpion venom with the unique ability to cross cell membranes, gaining access to intracellular targets. Ryanodine Receptors (RyR) are intracellular ion channels that ...Calcins are peptides from scorpion venom with the unique ability to cross cell membranes, gaining access to intracellular targets. Ryanodine Receptors (RyR) are intracellular ion channels that control release of Ca from the endoplasmic and sarcoplasmic reticulum. Calcins target RyRs and induce long-lived subconductance states, whereby single-channel currents are decreased. We used cryo-electron microscopy to reveal the binding and structural effects of imperacalcin, showing that it opens the channel pore and causes large asymmetry throughout the cytosolic assembly of the tetrameric RyR. This also creates multiple extended ion conduction pathways beyond the transmembrane region, resulting in subconductance. Phosphorylation of imperacalcin by protein kinase A prevents its binding to RyR through direct steric hindrance, showing how posttranslational modifications made by the host organism can determine the fate of a natural toxin. The structure provides a direct template for developing calcin analogs that result in full channel block, with potential to treat RyR-related disorders.
History
DepositionJul 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2024Group: Data collection / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / entity_src_nat
Item: _em_3d_fitting_list.initial_refinement_model_id
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Imperacalcin
G: Ryanodine receptor 1
H: Peptidyl-prolyl cis-trans isomerase FKBP1B
I: Calmodulin-1
A: Ryanodine receptor 1
B: Peptidyl-prolyl cis-trans isomerase FKBP1B
C: Calmodulin-1
D: Ryanodine receptor 1
E: Peptidyl-prolyl cis-trans isomerase FKBP1B
F: Calmodulin-1
J: Ryanodine receptor 1
K: Peptidyl-prolyl cis-trans isomerase FKBP1B
L: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,383,78929
Polymers2,380,56213
Non-polymers3,22716
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 1 types, 1 molecules M

#1: Protein/peptide Imperacalcin / IpCa / Imperatoxin activator / Imperatoxin-A / IpTxa


Mass: 3776.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pandinus imperator (emperor scorpion) / References: UniProt: P59868

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Protein , 3 types, 12 molecules GADJHBEKICFL

#2: Protein
Ryanodine receptor 1 / RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / ...RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal muscle-type ryanodine receptor / Type 1 ryanodine receptor


Mass: 565908.625 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P11716
#3: Protein
Peptidyl-prolyl cis-trans isomerase FKBP1B / PPIase FKBP1B / 12.6 kDa FK506-binding protein / FKBP-12.6 / FK506-binding protein 1B / FKBP-1B / ...PPIase FKBP1B / 12.6 kDa FK506-binding protein / FKBP-12.6 / FK506-binding protein 1B / FKBP-1B / Immunophilin FKBP12.6 / Rotamase / h-FKBP-12


Mass: 11667.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 / Production host: Escherichia coli (E. coli) / References: UniProt: P68106, peptidylprolyl isomerase
#4: Protein
Calmodulin-1


Mass: 16620.402 Da / Num. of mol.: 4 / Mutation: E32A, E68A, E105A, E141A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23

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Non-polymers , 4 types, 16 molecules

#5: Chemical
ChemComp-CFF / CAFFEINE / RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / ...RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal muscle-type ryanodine receptor / Type 1 ryanodine receptor / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H10N4O2 / Comment: medication*YM
#6: Chemical
ChemComp-CA / CALCIUM ION / RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / ...RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal muscle-type ryanodine receptor / Type 1 ryanodine receptor


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca
#7: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / ...RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal muscle-type ryanodine receptor / Type 1 ryanodine receptor


Mass: 507.181 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Chemical
ChemComp-ZN / ZINC ION / RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / ...RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal muscle-type ryanodine receptor / Type 1 ryanodine receptor


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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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: RyR1 in complex with ImperaCalcin in presence of Caffeine/CaM1234/Calcium/ATP
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Molecular weightValue: 2.2 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Oryctolagus cuniculus (rabbit)9986
31Pandinus imperator (emperor scorpion)55084
41Homo sapiens (human)9606
Buffer solutionpH: 7.4
SpecimenConc.: 10 mg/ml / Embedding 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: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
2crYOLO1.7.6particle selection
3EPUimage acquisition
8UCSF Chimeramodel fitting
10PHENIX1.20rc1-4392model refinement
12cryoSPARC3.2final Euler assignmentlocal Non-uniform refinement
13cryoSPARC3.2classification
14cryoSPARC3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144529 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 6M2W

6m2w


Accession code: 6M2W / Source name: PDB / Type: experimental model

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