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- PDB-8vk3: Structure of mouse RyR1 in complex with S100A1 (EGTA-only dataset) -

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Basic information

Entry
Database: PDB / ID: 8vk3
TitleStructure of mouse RyR1 in complex with S100A1 (EGTA-only dataset)
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP1A
  • Protein S100A1
  • Ryanodine receptor 1
KeywordsMEMBRANE PROTEIN / Calcium / Ion Channel
Function / homology
Function and homology information


junctional membrane complex / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / mTORC1-mediated signalling / activin receptor binding / cytoplasmic side of membrane / regulation of muscle contraction / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / regulation of response to osmotic stress ...junctional membrane complex / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / mTORC1-mediated signalling / activin receptor binding / cytoplasmic side of membrane / regulation of muscle contraction / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / regulation of response to osmotic stress / signaling receptor inhibitor activity / RAGE receptor binding / transforming growth factor beta receptor binding / Stimuli-sensing channels / type I transforming growth factor beta receptor binding / Ion homeostasis / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / ryanodine-sensitive calcium-release channel activity / I band / S100 protein binding / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to caffeine / ossification involved in bone maturation / ventricular cardiac muscle tissue morphogenesis / skin development / cellular response to ATP / regulation of heart contraction / FK506 binding / positive regulation of sprouting angiogenesis / cellular response to caffeine / outflow tract morphogenesis / organelle membrane / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / T cell proliferation / axon terminus / striated muscle contraction / heart morphogenesis / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / extrinsic component of cytoplasmic side of plasma membrane / Hsp70 protein binding / T-tubule / sarcoplasmic reticulum membrane / calcium channel complex / regulation of cytosolic calcium ion concentration / cellular response to calcium ion / sarcomere / peptidylprolyl isomerase / sarcoplasmic reticulum / peptidyl-prolyl cis-trans isomerase activity / muscle contraction / negative regulation of transforming growth factor beta receptor signaling pathway / calcium channel activity / sarcolemma / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / Z disc / calcium ion transport / calcium-dependent protein binding / cell cortex / ATPase binding / protein homotetramerization / positive regulation of canonical NF-kappaB signal transduction / protease binding / vesicle / transmembrane transporter binding / calmodulin binding / response to hypoxia / synapse / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / nucleoplasm / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein S100-A1 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / : / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 ...Protein S100-A1 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / : / 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. / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ryanodine receptor 1 / Peptidyl-prolyl cis-trans isomerase FKBP1A / Protein S100
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsWeninger, G. / 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 insights into the regulation of RyR1 by S100A1
Authors: Weninger, G.
History
DepositionJan 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: 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 1
E: Peptidyl-prolyl cis-trans isomerase FKBP1A
J: Protein S100A1
I: Protein S100A1
H: Peptidyl-prolyl cis-trans isomerase FKBP1A
F: Peptidyl-prolyl cis-trans isomerase FKBP1A
G: Peptidyl-prolyl cis-trans isomerase FKBP1A
K: Protein S100A1
M: Protein S100A1
O: Protein S100A1
L: Protein S100A1
N: Protein S100A1
P: Protein S100A1
D: Ryanodine receptor 1
B: Ryanodine receptor 1
C: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,401,22228
Polymers2,394,66316
Non-polymers6,55912
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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: 565692.562 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9PZQ0
#2: Protein
Peptidyl-prolyl cis-trans isomerase FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding ...PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 11939.629 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P26883, peptidylprolyl isomerase
#3: Protein
Protein S100A1 / S100 calcium-binding protein


Mass: 10516.784 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: S100a1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91V77
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*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 RyR1 with Calstabin-1 and S100A1 (EGTA condition)
Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110 mmol/LHEPES1
2150 mmol/Lsodium chlorideNaClSodium chloride1
30.25 %CHAPS1
40.01 %DOPC1
50.5 mmol/LTCEP1
65 mmol/LEGTA1
SpecimenConc.: 8.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.15 mmol/L S100A1-dimer
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12147

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36506 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003152156
ELECTRON MICROSCOPYf_angle_d0.602205948
ELECTRON MICROSCOPYf_dihedral_angle_d6.27120640
ELECTRON MICROSCOPYf_chiral_restr0.03722624
ELECTRON MICROSCOPYf_plane_restr0.00526772

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