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- EMDB-1275: The pore structure of the closed RyR1 channel. -

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Basic information

Entry
Database: EMDB / ID: EMD-1275
TitleThe pore structure of the closed RyR1 channel.
Map dataZ-axis of a 3D reconstruction coincides with the 4-fold axis of the channel complex
Sample
  • Sample: ryanodine receptor 1
  • Protein or peptide: Ryanodine receptor type 1
Function / homologyryanodine-sensitive calcium-release channel activity / RIH domain
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsLudtke SJ / Serysheva II / Hamilton SL / Chiu W
CitationJournal: Structure / Year: 2005
Title: The pore structure of the closed RyR1 channel.
Authors: Steven J Ludtke / Irina I Serysheva / Susan L Hamilton / Wah Chiu /
Abstract: Using single particle electron cryomicroscopy, several helices in the membrane-spanning region of RyR1, including an inner transmembrane helix, a short pore helix, and a helix parallel to the ...Using single particle electron cryomicroscopy, several helices in the membrane-spanning region of RyR1, including an inner transmembrane helix, a short pore helix, and a helix parallel to the membrane on the cytoplasmic side, have been clearly resolved. Our model places a highly conserved glycine (G4934) at the hinge position of the bent inner helix and two rings of negative charges at the luminal and cytoplasmic mouths of the pore. The kinked inner helix closely resembles the inner helix of the open MthK channel, suggesting that kinking alone does not open RyR1, as proposed for K+ channels.
History
DepositionJan 19, 2006-
Header (metadata) releaseOct 16, 2006-
Map releaseOct 16, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1275.gif

Downloads & links

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Map

FileDownload / File: emd_1275.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationZ-axis of a 3D reconstruction coincides with the 4-fold axis of the channel complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.81 Å/pix.
x 256 pix.
= 461.55 Å		1.81 Å/pix.
x 256 pix.
= 461.55 Å		1.81 Å/pix.
x 256 pix.
= 461.55 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.81 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.631 / Movie #1: 1
Minimum - Maximum-1.24222 - 2.25668
Average (Standard dev.)0.0636951 (±0.267637)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 461.55 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.811.811.81
M x/y/z255255255
origin x/y/z0.0000.0000.000
length x/y/z461.550461.550461.550
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-1.2422.2570.064

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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
  • Protein or peptide: Ryanodine receptor type 1

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Supramolecule #1000: ryanodine receptor 1

SupramoleculeName: ryanodine receptor 1 / type: sample / ID: 1000
Details: The sample was purified after solubilization with detergent from skeletal muscle cells
Oligomeric state: homotetramer / Number unique components: 1
Molecular weightTheoretical: 565 KDa

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Macromolecule #1: Ryanodine receptor type 1

MacromoleculeName: Ryanodine receptor type 1 / type: protein_or_peptide / ID: 1 / Name.synonym: Skeletal muscle calcium release channel / Details: detergent solubilized membrane protein / Number of copies: 4 / Oligomeric state: homotetramer / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Strain: White New Zealand / synonym: rabbit / Tissue: fast twitch skeletal muscle / Cell: muscle cell / Organelle: sarcoplasmic reticulum / Location in cell: sarcoplasmic reticulum membrane
Molecular weightExperimental: 565 KDa
SequenceGO: ryanodine-sensitive calcium-release channel activity / InterPro: RIH domain

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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 mg/mL
BufferpH: 7.4
Details: 20 mM Mops, 300 mM KCl, 1 mM DTT,0.4% CHAPS,5%sucrose,1mM EGTA
GridDetails: holey carbon 400 mesh Cu grid
VitrificationCryogen name: ETHANE / Chamber temperature: 101 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Thin carbon film supported by holey carbon film
Method: Blot for 3 second before plunging

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 96 K / Max: 97 K / Average: 96 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 400,000X
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 1.81 µm / Number real images: 869 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
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: 4.55 µm / Nominal defocus min: 1.37 µm / Nominal magnification: 60000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: CTF correction of each micrograph
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 28036
Final two d classificationNumber classes: 2294

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