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Archaeoglobus fulgidus methylation-guide sRNP
by single particle reconstruction, at 26 A resolution
#1: Surface view with section colored by density value, Surface level: 3, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 3, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5421 |
|---|---|
| Title | Archaeoglobus fulgidus methylation-guide sRNP |
| Map | Projection matching single particle reconstruction of Archaeoglobus fulgidus box C/D sRNP, 26 Angstrom resolution |
| Sample | Archaeoglobus fulgidus methylation-guide sRNP |
| Keywords |  archaea, box C/D sRNP, single particle EM, rRNA modification, RNA-protein complex, non-coding RNA |
| Authors | Bower-Phipps KR, Taylor DW, Wang HW, Baserga SJ |
| Date | Deposition: 2012-05-08, Header release: 2012-06-05, Map release: 2012-07-09, Last update: 2012-07-09 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 3, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 3, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | RNA, Vol. 18, Issue 8, Page 1527-40, Year 2012 |
|---|---|
| Title | The box C/D sRNP dimeric architecture is conserved across domain Archaea. |
| Authors | Kathleen R Bower-Phipps, David W Taylor, Hong-Wei Wang, Susan J Baserga Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA. |
| Keywords | Archaea (classification), Archaeal Proteins (chemistry), Base Sequence, Methylation, Molecular Sequence Data, Mutagenesis, Protein Binding, Protein Conformation, Protein Multimerization, RNA, Archaeal (genetics), RNA, Small Nucleolar (genetics), Ribonucleoproteins, Small Nucleolar (chemistry) |
| Links | DOI: 10.1261/rna.033134.112, PubMed: 22753779, PMC: PMC3404373 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5421.map ( map file in CCP4 format, 8390 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A= B= C: 345.6 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 2.7 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Projection matching single particle reconstruction of Archaeoglobus fulgidus box C/D sRNP, 26 Angstrom resolution | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | Archaeoglobus fulgidus methylation-guide sRNP |
|---|---|
| Number of Components | 1 |
| Oligomeric State | Four copies of each box C/D core protein could be docked in this map. |
| Theoretical Mass | 0.308MDa |
| Component #1: protein - box C/D sRNP | |
| Scientific name | ribonucleoprotein |
| Common Name | box C/D sRNP |
| Theoretical Mass | 0.308 MDa |
| Scientific Name of Species | Archaeoglobus fulgidus |
| NCBI taxonomy | 2234 |
| Recombinant expression | Yes |
 Experiment | |
| Sample Preparation | |
| Staining | 2% uranyl formate |
|---|---|
| Specimen State | particle |
| Buffer | Details: 20mM HEPES, 500mM NaCl, 1.5mM MgCl2 pH: 7.5 |
| Vitrification | |
| Cryogen Name | NONE |
| Instrument | NONE |
| Imaging | |
| Microscope | FEI TECNAI 12 |
| Date | 09-SEP-2011 |
| Details | low-dose conditions |
| Electron Gun | |
| Electron Source | LAB6 |
| Accelerating Voltage | 120 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 42000 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder | |
| Model | SIDE ENTRY, EUCENTRIC |
| Camera | |
| Detector | GATAN Ultra4000 4k x 4k CCD |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Projection matching |
| Software | SPIDER |
| Resolution By Author | 26 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 6336 |
| Atomic Model Fitting | |
| Model #0 | |
| Refinement Space | REAL |
| Software | Chimera, Situs |
| PDB Entry ID | 1RLG |
| Model #1 | |
| Refinement Space | REAL |
| Software | Chimera, Situs |
| PDB Entry ID | 1NT2 |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5421.xml (6.4 KB) | ||
|---|---|---|---|
| Map data | emd_5421.map.gz (5.8 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5421 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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