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The pore structure of the closed RyR1 channel.

by single particle reconstruction, at 9.6 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1275
TitleThe pore structure of the closed RyR1 channel.
MapZ-axis of a 3D reconstruction coincides with the 4-fold axis of the channel complex
Sampleryanodine receptor 1
AuthorsLudtke SJ, Serysheva II, Hamilton SL, Chiu W
DateDeposition: 2006-01-19, Header release: 2006-10-16, Map release: 2007-10-16, Last update: 2011-05-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleStructure, Vol. 13, Issue 8, Page 1203-11, Year 2005
TitleThe pore structure of the closed RyR1 channel.
AuthorsSteven J Ludtke, Irina I Serysheva, Susan L Hamilton, Wah Chiu
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
KeywordsAmino Acid Sequence, Animals, Cryoelectron Microscopy, Molecular Sequence Data, Muscle, Skeletal (metabolism), Protein Structure, Secondary, Protein Structure, Tertiary, Rabbits, Ryanodine Receptor Calcium Release Channel (chemistry), Structural Homology, Protein
LinksPII: S0969-2126(05)00215-7, DOI: 10.1016/j.str.2005.06.005, PubMed: 16084392, PMC: PMC2983469
Map
Fileemd_1275.map.gz ( map file in CCP4 format, 65537 KB )
Projections & SlicesSize of images:
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)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.631, 1 (movie #1):
Minimum - Maximum: -1.24222 - 2.25668
Average (Standard dev.): 0.0636951 (0.267637)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
Unit CellA= B= C: 461.55 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.81 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.2422.2570.064
Annotation DetailsZ-axis of a 3D reconstruction coincides with the 4-fold axis of the channel complex
Supplement
Images
Images
Sample
Nameryanodine receptor 1
Oligomeric Statehomotetramer
Number of Components1
Theoretical Mass0.565MDa
DetailsThe sample was purified after solubilization with detergent from skeletal muscle cells
Component #1: protein - Skeletal muscle calcium release channel
Scientific nameRyanodine receptor type 1
Common NameSkeletal muscle calcium release channel
Experimental Mass0.565 MDa
Detailsdetergent solubilized membrane protein
Oligomeric Detailshomotetramer
Number of Copies4
Scientific Name of SpeciesOryctolagus cuniculus

Common Name of Speciesrabbit
NCBI taxonomy9986
StrainWhite New Zealand
Recombinant expressionNo
Natural SourceCell: muscle cell
Organ Or Tissue: fast twitch skeletal muscle
Organelle: sarcoplasmic reticulum
Cell Location: sarcoplasmic reticulum membrane
LinksInter Pro: IPR:000699, Gene Ontology: GO:0005219
Experiment
Sample Preparation
Specimen Conc2 mg/ml
Specimen Support Detailsholey carbon 400 mesh Cu grid
Specimen Stateparticle
BufferDetails: 20 mM Mops, 300 mM KCl, 1 mM DTT,0.4% CHAPS,5%sucrose,1mM EGTA
pH: 7.4
Vitrification
Cryogen NameETHANE
Temperature101 Kelvin
InstrumentHOMEMADE PLUNGER
MethodBlot for 3 second before plunging
DetailsVitrification instrument: Thin carbon film supported by holey carbon film
Imaging
MicroscopeJEOL 2010F
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 60000
Astigmatismobjective lens astigmatism was corrected at 400,000X
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1370 nm - 4550 nm
Specimen Holder
Holderside entry
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature96 K ( 96 - 97 K)
Camera
DetectorGENERIC GATAN (4k x 4k)
Image Acquisition
Number of Digital Images869
Sampling Size1.81
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmIterative projection matching and Direct Fourier inversion
SoftwareEMAN
CTF CorrectionCTF correction of each micrograph
Resolution By Author9.6 A
Resolution MethodFSC 0.5
Single Particle
Number of Class Averages2294
Number of Projections28036
Applied SymmetryC4 (4 fold cyclic)
Download
Data from EMDB
Header (meta data in XML format)emd-1275.xml (8 KB)
Map dataemd_1275.map.gz (9.1 MB)
Images1275.gif (37.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1275
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 28.5 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 28.5 KB