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- PDB-6foo: Structure of Ryanodine Receptor 1 in nanodiscs in the presence of... -

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Basic information

Entry
Database: PDB / ID: 6foo
TitleStructure of Ryanodine Receptor 1 in nanodiscs in the presence of calcium and ATP
ComponentsRyanodine receptor 1
KeywordsMEMBRANE PROTEIN / calcium release channel / nanodiscs
Function / homologyRIH domain / B30.2/SPRY domain / Ryanodine receptor, SPRY domain 2 / Ryanodine receptor, SPRY domain 3 / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor 1 / MIR motif / Ryanodine receptor-related / EF-hand domain / Inositol 1,4,5-trisphosphate/ryanodine receptor ...RIH domain / B30.2/SPRY domain / Ryanodine receptor, SPRY domain 2 / Ryanodine receptor, SPRY domain 3 / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor 1 / MIR motif / Ryanodine receptor-related / EF-hand domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / Ryanodine receptor Ryr / SPRY domain / Ion transport domain / Ryanodine Receptor TM 4-6 / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Ryanodine receptor / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Mir domain superfamily / Inositol 1,4,5-trisphosphate/ryanodine receptor / Ryanodine Receptor TM 4-6 / EF-hand domain pair / B30.2/SPRY domain profile. / MIR domain profile. / MIR domain / RyR domain / RIH domain / SPRY domain / Ion transport protein / RyR and IP3R Homology associated / integral component of organelle membrane / ATP-gated ion channel activity / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / terminal cisterna / ryanodine receptor complex / ossification involved in bone maturation / cellular response to caffeine / calcium-release channel activity / skin development / voltage-gated calcium channel activity / outflow tract morphogenesis / sarcoplasmic reticulum membrane / release of sequestered calcium ion into cytosol / calcium channel activity / skeletal muscle fiber development / muscle contraction / calcium ion transmembrane transport / sarcoplasmic reticulum / toxic substance binding / cellular response to calcium ion / disordered domain specific binding / protein homotetramerization / drug binding / ion channel binding / calmodulin binding / calcium ion binding / membrane / integral component of membrane / ATP binding / identical protein binding / Ryanodine receptor 1
Function and homology information
Specimen sourceOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8.2 Å resolution
AuthorsWillegems, K. / Efremov, R.G.
CitationJournal: Structure / Year: 2018
Title: Influence of Lipid Mimetics on Gating of Ryanodine Receptor.
Authors: Katrien Willegems / Rouslan G Efremov
Abstract: Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) ...Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) reconstituted into lipid nanodiscs. RyR1 is a homotetrameric giant ion channel that couples excitation of muscle cells to fast calcium release from the sarcoplasmic reticulum. Using single-particle cryo-EM we show that RyR1 reconstituted into lipid nanodiscs is stabilized in the open conformation when bound to the plant toxin ryanodine, but not in the presence of its physiological activators, calcium and ATP. Further, using ryanodine binding assays we show that membrane mimetics influence RyR1 transition between closed and open-channel conformations. We find that all detergents, including fluorinated detergents added to nanodiscs, stabilize closed state of RyR1. Our biochemical results correlate with available structural data and suggest optimal conditions for structural studies of RyR1 gating.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 8, 2018 / Release: Aug 8, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 8, 2018Structure modelrepositoryInitial release
1.1Aug 15, 2018Structure modelData collection / Database references / Structure summarycitation / entity / entity_name_com_citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _entity_name_com.name

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Structure visualization

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Assembly

Deposited unit
A: Ryanodine receptor 1
B: Ryanodine receptor 1
C: Ryanodine receptor 1
D: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,131,1008
Polyers2,130,8394
Non-polymers2624
Water0
1


  • idetical with deposited unit
  • defined by software
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)21670
ΔGint (kcal/M)-122
Surface area (Å2)860680
MethodPISA

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Components

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


Mass: 532709.688 Da / Num. of mol.: 4 / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / Strain: New Zealand White rabbit / References: UniProt: P11716
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Formula: Zn / Zinc

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP
Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 2.2 MDa / Experimental value: NO
Source (natural)Cellular location: sarcoplasmic reticulum / Organism: Oryctolagus cuniculus (rabbit) / Strain: New Zealand white rabbit / Tissue: skeletal muscle
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer ID
120 mM3-morpholinopropane-1-sulfonic acidC7H15NO4S1
2200 mMsodium chlorideNaCl1
37 mMAdenosine triphosphateC10H16N5O13P31
41 mMDithiothreitolC4H10O2S21
50.2 mMEGTAC14H24N2O101
60.25 mMcalcium chlorideCaCl21
72 mg/mLfluorinated octyl maltosideC20H25F13O111
SpecimenConc.: 3 mg/ml / Details: Protein was reconstituted into lipid nanodiscs / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Chamber temperature: 293.15 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 92000 / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 1.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1906
Image scansSampling size: 14 microns / Width: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 1-16

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.12rc2_2821refinement
PHENIX1.12rc2_2821refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7PHENIXmodel fitting
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.12model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 90000
SymmetryPoint symmetry: C4
3D reconstructionResolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 42500 / Symmetry type: POINT
Atomic model buildingRef space: REAL
RefineStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00571221449151119676
ELECTRON MICROSCOPYf_angle_d1.01806561259163228
ELECTRON MICROSCOPYf_chiral_restr0.051443428966919112
ELECTRON MICROSCOPYf_plane_restr0.0071038295985121496
ELECTRON MICROSCOPYf_dihedral_angle_d9.9928179071771404

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