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- PDB-8uq5: Structure of human RyR2-S2808D in the primed state in the presenc... -

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Basic information

Entry
Database: PDB / ID: 8uq5
TitleStructure of human RyR2-S2808D in the primed state in the presence of Rapamycin
ComponentsRyanodine receptor 2
KeywordsMEMBRANE PROTEIN / calcium channel
Function / homology
Function and homology information


junctional sarcoplasmic reticulum membrane / 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 / regulation of AV node cell action potential / positive regulation of ATPase-coupled calcium transmembrane transporter activity ...junctional sarcoplasmic reticulum membrane / 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 / regulation of AV node cell action potential / positive regulation of ATPase-coupled calcium transmembrane transporter activity / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / regulation of cardiac muscle contraction by calcium ion signaling / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to muscle activity / calcium ion transport into cytosol / response to caffeine / cell communication by electrical coupling involved in cardiac conduction / response to redox state / positive regulation of heart rate / cellular response to caffeine / protein kinase A regulatory subunit binding / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / : / detection of calcium ion / striated muscle contraction / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / release of sequestered calcium ion into cytosol / cardiac muscle contraction / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / response to muscle stretch / regulation of heart rate / sarcoplasmic reticulum / establishment of localization in cell / calcium-mediated signaling / sarcolemma / calcium channel activity / Stimuli-sensing channels / intracellular calcium ion homeostasis / Z disc / : / calcium ion transport / transmembrane transporter binding / response to hypoxia / calmodulin binding / calcium ion binding / enzyme binding / protein-containing complex / membrane / identical protein binding / plasma membrane
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. / EF-hand domain pair / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Ryanodine receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsMiotto, M.C. / Marks, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL145473 United States
CitationJournal: To Be Published
Title: Structural basis for ryanodine receptor type 2 leak in heart failure and arrhythmogenic disorders
Authors: Miotto, M.C.
History
DepositionOct 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ryanodine receptor 2
B: Ryanodine receptor 2
C: Ryanodine receptor 2
D: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,265,57616
Polymers2,261,2574
Non-polymers4,31912
Water0
1


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

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Components

#1: Protein
Ryanodine receptor 2 /


Mass: 565314.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RYR2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q92736
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine 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
Has ligand of interestY

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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: Complex of RyR2-S2808D / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
Details: 30-minute incubation with rapamycin was stopped by flash freezing (vitrobot)
Buffer component
IDConc.NameFormulaBuffer-ID
1230 mMsodium chlorideNaClSodium chloride1
210 mMHEPESHEPES1
30.4 %CHAPSCHAPS1
41 mMEGTAEGTA1
50.5 mMtris(2-carboxyethyl)phosphineTCEP1
60.001 %DOPCDOPC1
710 mMATPAdenosine triphosphateATPAdenosine triphosphate1
80.25 mMrapamycinSirolimusRapamycinSirolimus1
SpecimenConc.: 2.5 mg/ml / Embedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1200 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 80 K
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selection
2Leginon3.5image acquisitionMSI-T2
4cryoSPARCCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
12cryoSPARCclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18232 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7UA5

7ua5


Accession code: 7UA5 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003138292
ELECTRON MICROSCOPYf_angle_d0.651186864
ELECTRON MICROSCOPYf_dihedral_angle_d5.35718328
ELECTRON MICROSCOPYf_chiral_restr0.04120500
ELECTRON MICROSCOPYf_plane_restr0.00623992

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