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The pore structure of the closed RyR1 channel.
by single particle reconstruction, at 9.6 A resolution
#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 / ID | EM DATA BANK (EMDB) / 1275 |
|---|---|
| Title | The pore structure of the closed RyR1 channel. |
| Map | Z-axis of a 3D reconstruction coincides with the 4-fold axis of the channel complex |
| Sample | ryanodine receptor 1 |
| Authors | Ludtke SJ, Serysheva II, Hamilton SL, Chiu W |
| Date | Deposition: 2006-01-19, Header release: 2006-10-16, Map release: 2007-10-16, Last update: 2011-05-26 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie 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 viewers |  Yorodumi,  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 | |
| Article | Structure, Vol. 13, Issue 8, Page 1203-11, Year 2005 |
|---|---|
| Title | The pore structure of the closed RyR1 channel. |
| Authors | Steven 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. |
| Keywords |  Amino 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 |
| Links | PII: S0969-2126(05)00215-7, DOI: 10.1016/j.str.2005.06.005, PubMed: 16084392, PMC: PMC2983469 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1275.map ( map file in CCP4 format, 67109 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | float (32-bit) | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A= B= C: 461.55 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 1.81 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Z-axis of a 3D reconstruction coincides with the 4-fold axis of the channel complex | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | ryanodine receptor 1 |
|---|---|
| Oligomeric State | homotetramer |
| Number of Components | 1 |
| Theoretical Mass | 0.565MDa |
| Details | The sample was purified after solubilization with detergent from skeletal muscle cells |
| Component #1: protein - Skeletal muscle calcium release channel | |
| Scientific name | Ryanodine receptor type 1 |
| Common Name | Skeletal muscle calcium release channel |
| Experimental Mass | 0.565 MDa |
| Details | detergent solubilized membrane protein |
| Oligomeric Details | homotetramer |
| Number of Copies | 4 |
| Scientific Name of Species | Oryctolagus cuniculus
|
| Common Name of Species | rabbit |
| NCBI taxonomy | 9986 |
| Strain | White New Zealand |
| Recombinant expression | No |
| Natural Source | Cell: muscle cell Organ Or Tissue: fast twitch skeletal muscle Organelle: sarcoplasmic reticulum Cell Location: sarcoplasmic reticulum membrane |
| Links | Inter Pro: IPR:000699, Gene Ontology: GO:0005219 |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 2 mg/ml |
|---|---|
| Specimen Support Details | holey carbon 400 mesh Cu grid |
| Specimen State | particle |
| Buffer | Details: 20 mM Mops, 300 mM KCl, 1 mM DTT,0.4% CHAPS,5%sucrose,1mM EGTA pH: 7.4 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Temperature | 101 Kelvin |
| Instrument | HOMEMADE PLUNGER |
| Method | Blot for 3 second before plunging |
| Details | Vitrification instrument: Thin carbon film supported by holey carbon film |
| Imaging | |
| Microscope | JEOL 2010F |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 15 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 60000 |
| Astigmatism | objective lens astigmatism was corrected at 400,000X |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1370 nm - 4550 nm |
| Specimen Holder | |
| Holder | side entry |
| Model | GATAN LIQUID NITROGEN |
| Tilt Angle | 0 degrees - 0 degrees |
| Temperature | 96 K ( 96 - 97 K) |
| Camera | |
| Detector | 4Kx4K GATAN CCD camera |
| Image Acquisition | |
| Number of Digital Images | 869 |
| Sampling Size | 1.81 |
| Quant Bit Number | 8 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Iterative projection matching and Direct Fourier inversion |
| Software | EMAN |
| CTF Correction | CTF correction of each micrograph |
| Resolution By Author | 9.6 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Class Averages | 2294 |
| Number of Projections | 28036 |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1275.xml (7.9 KB) | ||
|---|---|---|---|
| Map data | emd_1275.map.gz (9.1 MB) | ||
| Images |  1275.gif (37.1 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1275 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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