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

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Basic information

Entry
Database: EMDB / ID: 1275
TitleThe pore structure of the closed RyR1 channel.
Sampleryanodine receptor 1
SourceOryctolagus cuniculus / mammal / rabbit / アナウサギ /
Map dataZ-axis of a 3D reconstruction coincides with the 4-fold axis of the channel complex
Methodsingle particle reconstruction, at 9.6 A resolution
AuthorsLudtke SJ / Serysheva II / Hamilton SL / Chiu W
CitationStructure, 2005, 13, 1203-1211

Structure, 2005, 13, 1203-1211 StrPapers
The pore structure of the closed RyR1 channel.
Steven J Ludtke / Irina I Serysheva / Susan L Hamilton / Wah Chiu

DateDeposition: Jan 19, 2006 / Header (metadata) release: Oct 16, 2006 / Map release: Oct 16, 2007 / Last update: Jan 19, 2006

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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
  • Download
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Supplemental images

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Map

Fileemd_1275.map.gz (map file in CCP4 format, 65537 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.81 A/pix
= 461.55 A
256 pix
1.81 A/pix
= 461.55 A
256 pix
1.81 A/pix
= 461.55 A

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.81 A
Density
Contour Level:0.631, 1 (movie #1):
Minimum - Maximum-1.24222 - 2.25668
Average (Standard dev.)0.0636951 (0.267637)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
CellA=B=C: 461.55 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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
Details: The sample was purified after solubilization with detergent from skeletal muscle cells
Oligomeric State: homotetramer / Number of components: 1
MassTheoretical: 565 kDa

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Component #1: protein, Ryanodine receptor type 1

ProteinName: Ryanodine receptor type 1 / a.k.a: Skeletal muscle calcium release channel / Oligomeric Details: homotetramer / Details: detergent solubilized membrane protein / Recombinant expression: No / Number of Copies: 4
MassExperimental: 565 kDa
SourceSpecies: Oryctolagus cuniculus / mammal / rabbit / アナウサギ /
Strain: White New Zealand
Source (natural)Organelle: sarcoplasmic reticulum / Location in cell: sarcoplasmic reticulum membrane / Cell: muscle cell / Organ or tissue: fast twitch skeletal muscle
External referencesInterPro: InterPro: 000699 / Gene Ontology: GO: 0005219

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 2 mg/ml
Buffer solution: 20 mM Mops, 300 mM KCl, 1 mM DTT,0.4% CHAPS,5%sucrose,1mM EGTA
pH: 7.4
Support filmholey carbon 400 mesh Cu grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 101 K / Method: Blot for 3 second before plunging
Details: Vitrification instrument: Thin carbon film supported by holey carbon film

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Electron microscopy imaging

ImagingMicroscope: JEOL 2010F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 60000 X (nominal)
Astigmatism: objective lens astigmatism was corrected at 400,000X
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1370 - 4550 nm
Specimen HolderHolder: side entry / Model: GATAN LIQUID NITROGEN / Temperature: 96 K ( 96 - 97 K)
CameraDetector: GENERIC GATAN (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 869 / Sampling size: 1.81 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 2294 / Number of projections: 28036 / Applied symmetry: C4 (4 fold cyclic)
3D reconstructionAlgorithm: Iterative projection matching and Direct Fourier inversion
Software: EMAN / CTF correction: CTF correction of each micrograph / Resolution: 9.6 A / Resolution method: FSC 0.5

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