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- PDB-9znd: Structure of rabbit RyR1 complexed with FKBP12.6 and calmodulin i... -

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Basic information

Entry
Database: PDB / ID: 9znd
TitleStructure of rabbit RyR1 complexed with FKBP12.6 and calmodulin in the presence of dantrolene, ATP, 4-chloro-m-cresol, caffeine, and Mg2+
Components
  • Calmodulin-1
  • Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ryanodine receptor 1
KeywordsMEMBRANE PROTEIN / sarcoplasmic reticulum / intracellular calcium channel / excitation-contraction coupling / complex
Function / homology
Function and homology information


negative regulation of calcium-mediated signaling / ATP-gated ion channel activity / negative regulation of release of sequestered calcium ion into cytosol / response to redox state / ryanodine-sensitive calcium-release channel activity / terminal cisterna / CaM pathway / Cam-PDE 1 activation / negative regulation of heart rate / Sodium/Calcium exchangers ...negative regulation of calcium-mediated signaling / ATP-gated ion channel activity / negative regulation of release of sequestered calcium ion into cytosol / response to redox state / ryanodine-sensitive calcium-release channel activity / terminal cisterna / CaM pathway / Cam-PDE 1 activation / negative regulation of heart rate / Sodium/Calcium exchangers / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / Calmodulin induced events / ryanodine receptor complex / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / cellular response to caffeine / Loss of phosphorylation of MECP2 at T308 / skin development / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / CaMK IV-mediated phosphorylation of CREB / FK506 binding / 'de novo' protein folding / CASP4 inflammasome assembly / Glycogen breakdown (glycogenolysis) / negative regulation of ryanodine-sensitive calcium-release channel activity / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / : / organelle membrane / negative regulation of high voltage-gated calcium channel activity / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / outflow tract morphogenesis / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / smooth endoplasmic reticulum / Unblocking of NMDA receptors, glutamate binding and activation / intracellularly gated calcium channel activity / calcineurin-mediated signaling / RHO GTPases activate PAKs / regulation of cell communication by electrical coupling involved in cardiac conduction / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Regulation of MECP2 expression and activity / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / cellular response to interferon-beta / toxic substance binding / presynaptic cytosol / RHO GTPases activate IQGAPs / catalytic complex / calcium channel inhibitor activity / skeletal muscle fiber development / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of heart rate / Protein methylation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / titin binding / calcium channel complex / cellular response to calcium ion / voltage-gated potassium channel complex / FCERI mediated Ca+2 mobilization / muscle contraction / substantia nigra development / sarcoplasmic reticulum membrane / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / sperm midpiece / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of receptor signaling pathway via JAK-STAT / calyx of Held / Ras activation upon Ca2+ influx through NMDA receptor / adenylate cyclase activator activity / regulation of cytokinesis / VEGFR2 mediated cell proliferation / calcium-mediated signaling / spindle microtubule / VEGFR2 mediated vascular permeability / sarcomere / peptidylprolyl isomerase / sarcoplasmic reticulum
Similarity search - Function
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 ...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 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / 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 / 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
4-CHLORO-3-METHYLPHENOL / ADENOSINE-5'-TRIPHOSPHATE / CAFFEINE / : / Calmodulin-1 / Ryanodine receptor 1 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsKim, K. / Clarke, O.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01AR077720 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structural identification of the RY12 domain of RyR1 as an ADP sensor and the target of the malignant hyperthermia therapeutic dantrolene
Authors: Kim, K. / Li, H. / Yuan, Q. / Melville, Z. / Zalk, R. / des Georges, A. / Frank, J. / Hendrickson, W.A. / Marks, A.R. / Clarke, O.B.
History
DepositionDec 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,388,14952
Polymers2,377,46512
Non-polymers10,68440
Water30,5171694
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 12 molecules EFGHIJKLDBAC

#1: 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
#2: Protein
Calmodulin-1


Mass: 16790.434 Da / Num. of mol.: 4
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
#3: 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

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Non-polymers , 8 types, 1734 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-U1C / Dantrolene / 1-[(Z)-{[5-(4-nitrophenyl)furan-2-yl]methylidene}amino]imidazolidine-2,4-dione


Mass: 314.253 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H10N4O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-43M / 4-CHLORO-3-METHYLPHENOL


Mass: 142.583 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C7H7ClO / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#9: Chemical
ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10N4O2 / Comment: medication*YM
#10: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1694 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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 complexed with FKBP12.6 and calmodulin / Type: COMPLEX / Entity ID: #3, #1-#2 / Source: MULTIPLE SOURCES
Buffer solutionpH: 7.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 58 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71984 / Symmetry type: POINT
RefinementHighest resolution: 3.09 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004144496
ELECTRON MICROSCOPYf_angle_d0.587195928
ELECTRON MICROSCOPYf_dihedral_angle_d6.22920314
ELECTRON MICROSCOPYf_chiral_restr0.0421840
ELECTRON MICROSCOPYf_plane_restr0.00525432

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