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- PDB-5j8v: Structure of rabbit ryanodine receptor RyR1 open state activated ... -

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Basic information

Entry
Database: PDB / ID: 5j8v
TitleStructure of rabbit ryanodine receptor RyR1 open state activated by calcium ion
ComponentsRyanodine receptor 1
KeywordsTRANSPORT PROTEIN / endoplasmic reticula / skeletal muscles / intracellular calcium ion channel / activated by calcium ion
Function / homology
Function and homology information


ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis ...ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / toxic substance binding / voltage-gated calcium channel activity / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / muscle contraction / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / membrane / identical protein 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. / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsWang, X. / Wei, R. / Yin, C. / Sun, F.
Funding support China, 4items
OrganizationGrant numberCountry
Strategic Priority Research Program of Chinese Academy of SciencesXDB08030202 China
Ministry of Science & Technology of China2012CB917200 China
Ministry of Science & Technology of China2010CB912400 China
National Natural Science Foundation of China31270768 China
CitationJournal: Cell Res / Year: 2016
Title: Structural insights into Ca(2+)-activated long-range allosteric channel gating of RyR1.
Authors: Risheng Wei / Xue Wang / Yan Zhang / Saptarshi Mukherjee / Lei Zhang / Qiang Chen / Xinrui Huang / Shan Jing / Congcong Liu / Shuang Li / Guangyu Wang / Yaofang Xu / Sujie Zhu / Alan J ...Authors: Risheng Wei / Xue Wang / Yan Zhang / Saptarshi Mukherjee / Lei Zhang / Qiang Chen / Xinrui Huang / Shan Jing / Congcong Liu / Shuang Li / Guangyu Wang / Yaofang Xu / Sujie Zhu / Alan J Williams / Fei Sun / Chang-Cheng Yin /
Abstract: Ryanodine receptors (RyRs) are a class of giant ion channels with molecular mass over 2.2 mega-Daltons. These channels mediate calcium signaling in a variety of cells. Since more than 80% of the RyR ...Ryanodine receptors (RyRs) are a class of giant ion channels with molecular mass over 2.2 mega-Daltons. These channels mediate calcium signaling in a variety of cells. Since more than 80% of the RyR protein is folded into the cytoplasmic assembly and the remaining residues form the transmembrane domain, it has been hypothesized that the activation and regulation of RyR channels occur through an as yet uncharacterized long-range allosteric mechanism. Here we report the characterization of a Ca(2+)-activated open-state RyR1 structure by cryo-electron microscopy. The structure has an overall resolution of 4.9 Å and a resolution of 4.2 Å for the core region. In comparison with the previously determined apo/closed-state structure, we observed long-range allosteric gating of the channel upon Ca(2+) activation. In-depth structural analyses elucidated a novel channel-gating mechanism and a novel ion selectivity mechanism of RyR1. Our work not only provides structural insights into the molecular mechanisms of channel gating and regulation of RyRs, but also sheds light on structural basis for channel-gating and ion selectivity mechanisms for the six-transmembrane-helix cation channel family.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Advisory / Data collection / Category: em_software / pdbx_unobs_or_zero_occ_atoms / Item: _em_software.name
Revision 1.2Dec 11, 2019Group: Experimental preparation / Category: em_sample_support / Item: _em_sample_support.grid_type

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,263,6354
Polymers2,263,6354
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11360 Å2
ΔGint-117 kcal/mol
Surface area788970 Å2

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Components

#1: Protein
Ryanodine receptor 1 / / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal ...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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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: rabbit ryanodine receptor RyR1 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 2.2 MDa / Experimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.4
Details: 1:1000 diluted protease inhibitor cocktail was also added in buffer
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMsodium chlorideNaClSodium chloride1
22 mMdithiothreitolDTT1
32 mMphenylmethanesulfonyl fluoridePMSF1
420 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHepes1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Grids were blotted for 2s before plunging.

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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 FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 100286 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1300 nm / Calibrated defocus max: 5400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 80 K / Residual tilt: 23 mradians
Image recordingAverage exposure time: 2 sec. / Electron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 4931
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 31 / Used frames/image: 2-31

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7MDFFmodel fitting
10RELION1.4final Euler assignment
12RELION1.43D reconstruction
13Refmac5model refinement
Image processingDetails: The 31 frames of each video were processed into 10 images by merging 3 adjacent frames and then subjected into motion correction using program dosefgpu_driftcorr.
CTF correctionType: NONE
Particle selectionNum. of particles selected: 376537
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41743 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Atomic model buildingPDB-ID: 3J8H

3j8h


Pdb chain-ID: A / Pdb chain residue range: 1-5037

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