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- EMDB-5014: RyR1 in the closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-5014
TitleRyR1 in the closed state
Map data3D structure of RyR1 in the closed state.
Sample
  • Sample: ryanodine receptor 1
  • Organelle or cellular component: ryanodine receptor isoform 1
Keywordsryanodine receptor / ion channel gating
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.3 Å
AuthorsSamso M / Wagenknecht T / Allen PD
CitationJournal: Nat Struct Mol Biol / Year: 2005
Title: Internal structure and visualization of transmembrane domains of the RyR1 calcium release channel by cryo-EM.
Authors: Montserrat Samsó / Terence Wagenknecht / P D Allen /
Abstract: RyR1 is an intracellular calcium channel with a central role in muscle contraction. We obtained a three-dimensional reconstruction of the RyR1 in the closed state at a nominal resolution of ...RyR1 is an intracellular calcium channel with a central role in muscle contraction. We obtained a three-dimensional reconstruction of the RyR1 in the closed state at a nominal resolution of approximately 10 A using cryo-EM. The cytoplasmic assembly consists of a series of interconnected tubular structures that merge into four columns that extend into the transmembrane assembly. The transmembrane assembly, which has at least six transmembrane alpha-helices per monomer, has four tilted rods that can be fitted with the inner helices of a closed K(+) channel atomic structure. The rods splay out at the lumenal side and converge into a dense ring at the cytoplasmic side. Another set of four rods emerges from this ring and shapes the inner part of the four columns. The resulting constricted axial structure provides direct continuity between cytoplasmic and transmembrane assemblies, and a possible mechanism for control of channel gating through conformational changes in the cytoplasmic assembly.
History
DepositionJun 17, 2008-
Header (metadata) releaseJun 23, 2008-
Map releaseApr 23, 2009-
UpdateJan 6, 2011-
Current statusJan 6, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.28
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5014_1.png

Downloads & links

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Map

FileDownload / File: emd_5014.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D structure of RyR1 in the closed state.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 180 pix.
= 504. Å		2.8 Å/pix.
x 180 pix.
= 504. Å		2.8 Å/pix.
x 180 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0707 / Movie #1: 0.28
Minimum - Maximum-0.111036 - 0.660459
Average (Standard dev.)0.00770472 (±0.0687097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 504 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z504.000504.000504.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1110.6600.008

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Supplemental data

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Sample components

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Entire : ryanodine receptor 1

EntireName: ryanodine receptor 1
Components
  • Sample: ryanodine receptor 1
  • Organelle or cellular component: ryanodine receptor isoform 1

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Supramolecule #1000: ryanodine receptor 1

SupramoleculeName: ryanodine receptor 1 / type: sample / ID: 1000 / Oligomeric state: homotetramer / Number unique components: 1
Molecular weightTheoretical: 565 KDa

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Supramolecule #1: ryanodine receptor isoform 1

SupramoleculeName: ryanodine receptor isoform 1 / type: organelle_or_cellular_component / ID: 1 / Name.synonym: RyR1 / Number of copies: 4 / Oligomeric state: Tetramer / Recombinant expression: No / Database: NCBI
Ref GO0: GO:0005219
Ref INTERPRO0: IPR000699
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit / Tissue: fast twitch skeletal muscle / Organelle: sarcoplasmic reticulum / Location in cell: sarcoplasmic reticulum membrane
Molecular weightExperimental: 565 KDa / Theoretical: 565 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.00 mg/mL
BufferpH: 7.4
Details: 20 mM Na-MOPS pH 7.4, 0.9 M NaCl, 0.5% (w/v) CHAPS, 2 mM DTT, 2 mM EGTA
GridDetails: 300 mesh holey copper grids
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: two-side blotting plunger
Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 87 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 818 / Average electron dose: 10 e/Å2 / Details: after scanning pixels were averaged 2x2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.3 Å / Resolution method: OTHER / Software - Name: FREALIGN and SPIDER / Number images used: 25722

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Atomic model buiding 1

Initial modelPDB ID:

1bl8

DetailsThe inner helices of KcsA (residues 72-119) were fitted by manual docking to the inner helices of RyR1 using program Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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