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- EMDB-33940: Structure of recombinant RyR2 (Ca2+ dataset, class 3, open state) -

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Basic information

Entry
Database: EMDB / ID: EMD-33940
TitleStructure of recombinant RyR2 (Ca2+ dataset, class 3, open state)
Map dataStructure of recombinant RyR2 (Ca2 dataset, class 3, open state)
Sample
  • Complex: Recombinant RyR2 in the presence of EGTA
    • Complex: Ryanodine receptor 2
    • Complex: FKBP1B
Function / homology
Function and homology information


manganese ion transmembrane transport / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / organic cyclic compound binding / regulation of AV node cell action potential ...manganese ion transmembrane transport / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / organic cyclic compound binding / regulation of AV node cell action potential / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / Stimuli-sensing channels / Ion homeostasis / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / embryonic heart tube morphogenesis / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of cardiac muscle contraction by calcium ion signaling / cardiac muscle hypertrophy / ryanodine-sensitive calcium-release channel activity / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to muscle activity / calcium ion transmembrane import into cytosol / calcium ion transport into cytosol / A band / response to caffeine / cell communication by electrical coupling involved in cardiac conduction / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / positive regulation of heart rate / negative regulation of phosphoprotein phosphatase activity / FK506 binding / negative regulation of cytosolic calcium ion concentration / positive regulation of axon regeneration / cellular response to caffeine / intracellularly gated calcium channel activity / protein kinase A regulatory subunit binding / smooth endoplasmic reticulum / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / response to magnesium ion / : / detection of calcium ion / smooth muscle contraction / striated muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / response to vitamin E / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / protein peptidyl-prolyl isomerization / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / cardiac muscle contraction / cellular response to epinephrine stimulus / sarcoplasmic reticulum membrane / calcium channel complex / regulation of cytosolic calcium ion concentration / response to muscle stretch / extrinsic component of cytoplasmic side of plasma membrane / regulation of heart rate / monoatomic ion transmembrane transport / sarcomere / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / establishment of localization in cell / calcium ion transmembrane transport / sarcolemma / calcium channel activity / response to hydrogen peroxide / Stimuli-sensing channels / intracellular calcium ion homeostasis / Z disc / response to calcium ion / calcium ion transport / : / nuclear envelope / positive regulation of cytosolic calcium ion concentration / protein refolding / scaffold protein binding / transmembrane transporter binding / response to hypoxia / calmodulin binding / signaling receptor binding / calcium ion binding / protein kinase binding / enzyme binding
Similarity search - Function
: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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 junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / EF-hand domain pair / Ion transport domain / Ion transport protein / EF-hand domain / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 2 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsKobayashi T / Tsutsumi A / Kurebayashi N / Kodama M / Kikkawa M / Murayama T / Ogawa H
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16H04748 Japan
Japan Society for the Promotion of Science (JSPS)JP19K07105 Japan
Japan Society for the Promotion of Science (JSPS)19H03404 Japan
Japan Society for the Promotion of Science (JSPS)JP21H02411 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101080 Japan
Japan Agency for Medical Research and Development (AMED)19ek0109202 Japan
CitationJournal: Nat Commun / Year: 2022
Title: Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations.
Authors: Takuya Kobayashi / Akihisa Tsutsumi / Nagomi Kurebayashi / Kei Saito / Masami Kodama / Takashi Sakurai / Masahide Kikkawa / Takashi Murayama / Haruo Ogawa /
Abstract: Cardiac ryanodine receptor (RyR2) is a large Ca release channel in the sarcoplasmic reticulum and indispensable for excitation-contraction coupling in the heart. RyR2 is activated by Ca and RyR2 ...Cardiac ryanodine receptor (RyR2) is a large Ca release channel in the sarcoplasmic reticulum and indispensable for excitation-contraction coupling in the heart. RyR2 is activated by Ca and RyR2 mutations are implicated in severe arrhythmogenic diseases. Yet, the structural basis underlying channel opening and how mutations affect the channel remains unknown. Here, we address the gating mechanism of RyR2 by combining high-resolution structures determined by cryo-electron microscopy with quantitative functional analysis of channels carrying various mutations in specific residues. We demonstrated two fundamental mechanisms for channel gating: interactions close to the channel pore stabilize the channel to prevent hyperactivity and a series of interactions in the surrounding regions is necessary for channel opening upon Ca binding. Mutations at the residues involved in the former and the latter mechanisms cause gain-of-function and loss-of-function, respectively. Our results reveal gating mechanisms of the RyR2 channel and alterations by pathogenic mutations at the atomic level.
History
DepositionJul 29, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33940.png

Downloads & links

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Map

FileDownload / File: emd_33940.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of recombinant RyR2 (Ca2 dataset, class 3, open state)
Voxel sizeX=Y=Z: 1.239 Å
Density
Contour LevelBy AUTHOR: 0.021
Minimum - Maximum-0.084175974 - 0.11878833
Average (Standard dev.)-4.8635484e-05 (±0.005413515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 421.25998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Structure of recombinant RyR2 (Ca2 dataset, class 3, open state)

Fileemd_33940_half_map_1.map
AnnotationStructure of recombinant RyR2 (Ca2 dataset, class 3, open state)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Structure of recombinant RyR2 (Ca2 dataset, class 3, open state)

Fileemd_33940_half_map_2.map
AnnotationStructure of recombinant RyR2 (Ca2 dataset, class 3, open state)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Recombinant RyR2 in the presence of EGTA

EntireName: Recombinant RyR2 in the presence of EGTA
Components
  • Complex: Recombinant RyR2 in the presence of EGTA
    • Complex: Ryanodine receptor 2
    • Complex: FKBP1B

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Supramolecule #1: Recombinant RyR2 in the presence of EGTA

SupramoleculeName: Recombinant RyR2 in the presence of EGTA / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: in complex with FKBP12.6
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #2: Ryanodine receptor 2

SupramoleculeName: Ryanodine receptor 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: FKBP1B

SupramoleculeName: FKBP1B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Sugar embeddingMaterial: buffer
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5tal

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40665

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