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- EMDB-4258: Structure of Ryanodine receptor 1 in nanodiscs in the presence of... -

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Basic information

Entry
Database: EMDB / ID: 4258
TitleStructure of Ryanodine receptor 1 in nanodiscs in the presence of calcium, ATP and ryanodine
Map data
SampleRyanodine receptor 1 reconstituted in lipid nanodiscs in the presence of calcium, ATP and ryanodine:
Ryanodine receptor 1 / (ligand) x 2
Function / homologyRIH domain / B30.2/SPRY domain / Ryanodine receptor, SPRY domain 2 / Ryanodine receptor, SPRY domain 3 / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor 1 / MIR motif / Ryanodine receptor-related / EF-hand domain / Inositol 1,4,5-trisphosphate/ryanodine receptor ...RIH domain / B30.2/SPRY domain / Ryanodine receptor, SPRY domain 2 / Ryanodine receptor, SPRY domain 3 / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor 1 / MIR motif / Ryanodine receptor-related / EF-hand domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / Ryanodine receptor Ryr / SPRY domain / Ion transport domain / Ryanodine Receptor TM 4-6 / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Ryanodine receptor / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Mir domain superfamily / Inositol 1,4,5-trisphosphate/ryanodine receptor / Ryanodine Receptor TM 4-6 / EF-hand domain pair / B30.2/SPRY domain profile. / MIR domain profile. / MIR domain / RyR domain / RIH domain / SPRY domain / Ion transport protein / RyR and IP3R Homology associated / integral component of organelle membrane / ATP-gated ion channel activity / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / terminal cisterna / ryanodine receptor complex / ossification involved in bone maturation / cellular response to caffeine / calcium-release channel activity / skin development / voltage-gated calcium channel activity / outflow tract morphogenesis / sarcoplasmic reticulum membrane / release of sequestered calcium ion into cytosol / calcium channel activity / skeletal muscle fiber development / muscle contraction / calcium ion transmembrane transport / sarcoplasmic reticulum / toxic substance binding / cellular response to calcium ion / disordered domain specific binding / protein homotetramerization / drug binding / ion channel binding / calmodulin binding / calcium ion binding / membrane / integral component of membrane / ATP binding / identical protein binding / Ryanodine receptor 1
Function and homology information
SourceOryctolagus cuniculus (rabbit) / Rabbit (rabbit)
Methodsingle particle reconstruction / cryo EM / 7.3 Å resolution
AuthorsWillegems K / Efremov RG
CitationJournal: Structure / Year: 2018
Title: Influence of Lipid Mimetics on Gating of Ryanodine Receptor.
Authors: Katrien Willegems / Rouslan G Efremov
Abstract: Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) ...Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) reconstituted into lipid nanodiscs. RyR1 is a homotetrameric giant ion channel that couples excitation of muscle cells to fast calcium release from the sarcoplasmic reticulum. Using single-particle cryo-EM we show that RyR1 reconstituted into lipid nanodiscs is stabilized in the open conformation when bound to the plant toxin ryanodine, but not in the presence of its physiological activators, calcium and ATP. Further, using ryanodine binding assays we show that membrane mimetics influence RyR1 transition between closed and open-channel conformations. We find that all detergents, including fluorinated detergents added to nanodiscs, stabilize closed state of RyR1. Our biochemical results correlate with available structural data and suggest optimal conditions for structural studies of RyR1 gating.
Validation ReportPDB-ID: 6fg3

SummaryFull report
PDB-ID: 6foo

SummaryFull report
About validation report
DateDeposition: Jan 9, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Aug 8, 2018 / Last update: Aug 15, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6fg3
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4258.map.gz (map file in CCP4 format, 219489 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
380 pix
1.36 Å/pix.
= 514.9 Å
380 pix
1.36 Å/pix.
= 514.9 Å
380 pix
1.36 Å/pix.
= 514.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.355 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.08701025 - 0.21704483
Average (Standard dev.)0.0007965246 (0.00919777)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions380380380
Origin0.0.0.
Limit379.379.379.
Spacing380380380
CellA=B=C: 514.9 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3551.3551.355
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z514.900514.900514.900
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0870.2170.001

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Supplemental data

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Sample components

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Entire Ryanodine receptor 1 reconstituted in lipid nanodiscs in the pres...

EntireName: Ryanodine receptor 1 reconstituted in lipid nanodiscs in the presence of calcium, ATP and ryanodine
Number of components: 4

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Component #1: protein, Ryanodine receptor 1 reconstituted in lipid nanodiscs in...

ProteinName: Ryanodine receptor 1 reconstituted in lipid nanodiscs in the presence of calcium, ATP and ryanodine
Recombinant expression: No
MassTheoretical: 2.2 MDa
SourceSpecies: Oryctolagus cuniculus (rabbit) / Strain: New Zealand white rabbit

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Component #2: protein, Ryanodine receptor 1

ProteinName: Ryanodine receptor 1
Details: Poly Unk stretches correspond to polypeptide regions where the register is not assigned.
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 532.033062 kDa
SourceSpecies: Rabbit (rabbit) / Strain: New Zealand white rabbit
Source (natural)Organ or tissue: skeletal muscle

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Component #3: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #4: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / pH: 7.4
Support filmGlow discharged in ELMO plasma cleaner at current of 3 mA for 1 min.
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 293.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 28 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000. X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 3000.0 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3078 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 61773
3D reconstructionResolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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