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- PDB-8seo: Cryo-EM Structure of RyR1 + ATP-gamma-S -

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Basic information

Entry
Database: PDB / ID: 8seo
TitleCryo-EM Structure of RyR1 + ATP-gamma-S
Components
  • Glutathione S-transferase class-mu 26 kDa isozyme,Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ryanodine receptor 1
KeywordsTRANSPORT PROTEIN / Calcium ion channel / skeletal muscle / nucleotide / homotetramer
Function / homology
Function and homology information


ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / negative regulation of insulin secretion involved in cellular response to glucose stimulus / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus ...ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / negative regulation of insulin secretion involved in cellular response to glucose stimulus / ryanodine receptor complex / 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 / ossification involved in bone maturation / cell communication by electrical coupling involved in cardiac conduction / response to redox state / protein maturation by protein folding / skin development / 'de novo' protein folding / negative regulation of heart rate / negative regulation of phosphoprotein phosphatase activity / FK506 binding / positive regulation of axon regeneration / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / glutathione transferase / : / glutathione transferase activity / toxic substance binding / smooth muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / response to vitamin E / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / skeletal muscle fiber development / 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 / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / regulation of cytosolic calcium ion concentration / cellular response to calcium ion / sarcoplasmic reticulum / muscle contraction / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / calcium channel activity / response to hydrogen peroxide / intracellular calcium ion homeostasis / Stimuli-sensing channels / Z disc / disordered domain specific binding / positive regulation of cytosolic calcium ion concentration / protein refolding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / signaling receptor binding / calcium ion binding / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
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 / Glutathione S-transferase, C-terminal 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. / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Glutathione S-transferase class-mu 26 kDa isozyme / Ryanodine receptor 1 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsCholak, S. / Saville, J.W. / Zhu, X. / Berezuk, A.M. / Tuttle, K.S. / Haji-Ghassemi, O. / Van Petegem, F. / Subramaniam, S.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canada Excellence Research Chair Award Canada
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Structure / Year: 2023
Title: Allosteric modulation of ryanodine receptor RyR1 by nucleotide derivatives.
Authors: Spencer Cholak / James W Saville / Xing Zhu / Alison M Berezuk / Katharine S Tuttle / Omid Haji-Ghassemi / Francisco J Alvarado / Filip Van Petegem / Sriram Subramaniam /
Abstract: The coordinated release of Ca from the sarcoplasmic reticulum (SR) is critical for excitation-contraction coupling. This release is facilitated by ryanodine receptors (RyRs) that are embedded in the ...The coordinated release of Ca from the sarcoplasmic reticulum (SR) is critical for excitation-contraction coupling. This release is facilitated by ryanodine receptors (RyRs) that are embedded in the SR membrane. In skeletal muscle, activity of RyR1 is regulated by metabolites such as ATP, which upon binding increase channel open probability (P). To obtain structural insights into the mechanism of RyR1 priming by ATP, we determined several cryo-EM structures of RyR1 bound individually to ATP-γ-S, ADP, AMP, adenosine, adenine, and cAMP. We demonstrate that adenine and adenosine bind RyR1, but AMP is the smallest ATP derivative capable of inducing long-range (>170 Å) structural rearrangements associated with channel activation, establishing a structural basis for key binding site interactions that are the threshold for triggering quaternary structural changes. Our finding that cAMP also induces these structural changes and results in increased channel opening suggests its potential role as an endogenous modulator of RyR1 conductance.
History
DepositionApr 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ryanodine receptor 1
B: Ryanodine receptor 1
C: Ryanodine receptor 1
D: Ryanodine receptor 1
E: Glutathione S-transferase class-mu 26 kDa isozyme,Peptidyl-prolyl cis-trans isomerase FKBP1B
F: Glutathione S-transferase class-mu 26 kDa isozyme,Peptidyl-prolyl cis-trans isomerase FKBP1B
G: Glutathione S-transferase class-mu 26 kDa isozyme,Peptidyl-prolyl cis-trans isomerase FKBP1B
H: Glutathione S-transferase class-mu 26 kDa isozyme,Peptidyl-prolyl cis-trans isomerase FKBP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,426,16916
Polymers2,423,8158
Non-polymers2,3558
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "C" and (resid 11 through 1230 or resid 1232...
d_2ens_1(chain "B" and (resid 11 through 1230 or resid 1232...
d_3ens_1(chain "D" and (resid 11 through 1230 or resid 1232...
d_4ens_1(chain "A" and (resid 11 through 1230 or resid 1232...
d_1ens_2chain "E"
d_2ens_2chain "F"
d_3ens_2chain "G"
d_4ens_2chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALMETMETCC11 - 123011 - 1230
d_12ens_1ARGARGTHRTHRCC1232 - 17421232 - 1742
d_13ens_1ALAALASERSERCC1744 - 20991744 - 2099
d_14ens_1METMETMETMETCC2101 - 22672101 - 2267
d_15ens_1GLYGLYLEULEUCC2269 - 23682269 - 2368
d_16ens_1GLYGLYLEULEUCC2370 - 25832370 - 2583
d_17ens_1THRTHRCYSCYSCC2585 - 26112585 - 2611
d_18ens_1TYRTYRARGARGCC2613 - 28692613 - 2869
d_19ens_1LEULEUALAALACC2871 - 34212871 - 3421
d_110ens_1TRPTRPSERSERCC3423 - 50373423 - 5037
d_111ens_1AGSAGSAGSAGSCM5101
d_21ens_1VALVALMETMETBB11 - 123011 - 1230
d_22ens_1ARGARGTHRTHRBB1232 - 17421232 - 1742
d_23ens_1ALAALASERSERBB1744 - 20991744 - 2099
d_24ens_1METMETMETMETBB2101 - 22672101 - 2267
d_25ens_1GLYGLYLEULEUBB2269 - 23682269 - 2368
d_26ens_1GLYGLYLEULEUBB2370 - 25832370 - 2583
d_27ens_1THRTHRCYSCYSBB2585 - 26112585 - 2611
d_28ens_1TYRTYRARGARGBB2613 - 28692613 - 2869
d_29ens_1LEULEUALAALABB2871 - 34212871 - 3421
d_210ens_1TRPTRPSERSERBB3423 - 50373423 - 5037
d_211ens_1AGSAGSAGSAGSBK5101
d_31ens_1VALVALMETMETDD11 - 123011 - 1230
d_32ens_1ARGARGTHRTHRDD1232 - 17421232 - 1742
d_33ens_1ALAALASERSERDD1744 - 20991744 - 2099
d_34ens_1METMETMETMETDD2101 - 22672101 - 2267
d_35ens_1GLYGLYLEULEUDD2269 - 23682269 - 2368
d_36ens_1GLYGLYLEULEUDD2370 - 25832370 - 2583
d_37ens_1THRTHRCYSCYSDD2585 - 26112585 - 2611
d_38ens_1TYRTYRARGARGDD2613 - 28692613 - 2869
d_39ens_1LEULEUALAALADD2871 - 34212871 - 3421
d_310ens_1TRPTRPSERSERDD3423 - 50373423 - 5037
d_311ens_1AGSAGSAGSAGSDO5101
d_41ens_1VALVALMETMETAA11 - 123011 - 1230
d_42ens_1ARGARGTHRTHRAA1232 - 17421232 - 1742
d_43ens_1ALAALASERSERAA1744 - 20991744 - 2099
d_44ens_1METMETMETMETAA2101 - 22672101 - 2267
d_45ens_1GLYGLYLEULEUAA2269 - 23682269 - 2368
d_46ens_1GLYGLYLEULEUAA2370 - 25832370 - 2583
d_47ens_1THRTHRCYSCYSAA2585 - 26112585 - 2611
d_48ens_1TYRTYRARGARGAA2613 - 28692613 - 2869
d_49ens_1LEULEUALAALAAA2871 - 34212871 - 3421
d_410ens_1TRPTRPSERSERAA3423 - 50373423 - 5037
d_411ens_1AGSAGSAGSAGSAI5101
d_11ens_2GLYGLYGLUGLUEE1 - 107244 - 350
d_21ens_2GLYGLYGLUGLUFF1 - 107244 - 350
d_31ens_2GLYGLYGLUGLUGG1 - 107244 - 350
d_41ens_2GLYGLYGLUGLUHH1 - 107244 - 350

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(2.36439501311E-8, 1, 3.12717059437E-8), (-1, 2.36439574586E-8, -2.35562900521E-7), (-2.35562901261E-7, -3.12717003741E-8, 1)-1.68914248775E-5, 515.200050417, 7.63789815323E-5
2given(-3.30306941354E-7, -1, 1.94916530106E-7), (1, -3.30306881624E-7, 3.06300150377E-7), (-3.06300085995E-7, 1.94916631279E-7, 1)515.200067769, 2.16365752976E-5, 0.000118117721172
3given(-0.999999873136, -0.000435718707204, 0.00025273830137), (0.000435966615526, -0.999999423133, 0.000981665080818), (0.000252310425734, 0.000981775141742, 0.999999486228)515.231424456, 514.786262295, -0.312060365438
4given(-2.16722301396E-5, -0.999999999428, 2.59657660999E-5), (0.999999999433, -2.16728994161E-5, -2.57753398603E-5), (2.5775902599E-5, 2.59652074761E-5, 0.999999999331)515.196818635, 0.0154244108046, -0.0146108824506
5given(-0.999999999442, 2.12639484046E-5, 2.57568350609E-5), (-2.12632866187E-5, -0.999999999444, 2.56936047794E-5), (2.57573813941E-5, 2.56930570901E-5, 0.999999999338)515.184727388, 515.196820266, -0.0145070310659
6given(1), (-1), (1)5.11590769747E-13, 515.2, -1.70530256582E-13

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Components

#1: Protein
Ryanodine receptor 1 / / RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / ...RYR-1 / 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
#2: Protein
Glutathione S-transferase class-mu 26 kDa isozyme,Peptidyl-prolyl cis-trans isomerase FKBP1B / GST 26 / Sj26 antigen / SjGST / PPIase FKBP1B / 12.6 kDa FK506-binding protein / 12.6 kDa FKBP / ...GST 26 / Sj26 antigen / SjGST / PPIase FKBP1B / 12.6 kDa FK506-binding protein / 12.6 kDa FKBP / FKBP-12.6 / FK506-binding protein 1B / FKBP-1B / Immunophilin FKBP12.6 / Rotamase / h-FKBP-12


Mass: 40045.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 / Production host: Escherichia coli (E. coli)
References: UniProt: P08515, UniProt: P68106, glutathione transferase, peptidylprolyl isomerase
#3: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
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: RyR1 in complex with FKBP12.6Ryanodine receptor 1 / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 96000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 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
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM softwareName: EPU / Version: 3.3 / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55892 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 283.26 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0053146280
ELECTRON MICROSCOPYf_angle_d1.0566198164
ELECTRON MICROSCOPYf_chiral_restr0.060121780
ELECTRON MICROSCOPYf_plane_restr0.007225756
ELECTRON MICROSCOPYf_dihedral_angle_d14.806154592
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints1.52634996916E-12
ens_1d_3CCELECTRON MICROSCOPYNCS constraints1.87222494733E-12
ens_1d_4CCELECTRON MICROSCOPYNCS constraints9.2406563808E-12
ens_2d_2EEELECTRON MICROSCOPYNCS constraints2.18768514304E-11
ens_2d_3EEELECTRON MICROSCOPYNCS constraints5.04211097548E-13
ens_2d_4EEELECTRON MICROSCOPYNCS constraints2.25550923982E-13

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