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- PDB-5go9: Cryo-EM structure of RyR2 in closed state -

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Basic information

Entry
Database: PDB / ID: 5go9
TitleCryo-EM structure of RyR2 in closed state
ComponentsRyR2Ryanodine receptor 2
KeywordsTRANSPORT PROTEIN / Membrane protein / Channel
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsPeng, W. / Wu, J.P. / Yan, N.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2015CB9101012014, 2016YFA0500402, ZX09507003006 China
National Natural Science Foundation of Chinaproject 31321062, 31021002, 31611130036 China
CitationJournal: Science / Year: 2016
Title: Structural basis for the gating mechanism of the type 2 ryanodine receptor RyR2.
Authors: Wei Peng / Huaizong Shen / Jianping Wu / Wenting Guo / Xiaojing Pan / Ruiwu Wang / S R Wayne Chen / Nieng Yan /
Abstract: RyR2 is a high-conductance intracellular calcium (Ca) channel that controls the release of Ca from the sarco(endo)plasmic reticulum of a variety of cells. Here, we report the structures of RyR2 from ...RyR2 is a high-conductance intracellular calcium (Ca) channel that controls the release of Ca from the sarco(endo)plasmic reticulum of a variety of cells. Here, we report the structures of RyR2 from porcine heart in both the open and closed states at near-atomic resolutions determined using single-particle electron cryomicroscopy. Structural comparison reveals a breathing motion of the overall cytoplasmic region resulted from the interdomain movements of amino-terminal domains (NTDs), Helical domains, and Handle domains, whereas almost no intradomain shifts are observed in these armadillo repeats-containing domains. Outward rotations of the Central domains, which integrate the conformational changes of the cytoplasmic region, lead to the dilation of the cytoplasmic gate through coupled motions. Our structural and mutational characterizations provide important insights into the gating and disease mechanism of RyRs.
History
DepositionJul 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / em_image_scans / Item: _cell.Z_PDB
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: RyR2
B: RyR2
C: RyR2
D: RyR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,259,8848
Polymers2,259,6234
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area23320 Å2
ΔGint-114 kcal/mol
Surface area612090 Å2

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Components

#1: Protein
RyR2 / Ryanodine receptor 2


Mass: 564905.625 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Sequence detailsThe reference sequence database does not currently exist.

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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: RyR2Ryanodine receptor 2 / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 2.2 MDa / Experimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
Details: 25 mM Tris, pH 7.5, 300 mM NaCl, 0.1 % Digitonin, 2 mM DTT, 5mM EDTA, and protease inhibitors.
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Zhongjingkeyi Technology
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K
Details: Grids were immediately blotted for 1.5 s and flash-frozen in liquid 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 FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingElectron dose: 44 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND3CTF correction
9REFMAC5.8model refinement
12RELION1.4classification
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48454 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL

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