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Yorodumi- EMDB-1806: Cryo-electron tomography derived density map of a conserved retro... -
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-Basic information
Entry | Database: EMDB / ID: EMD-1806 | |||||||||
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Title | Cryo-electron tomography derived density map of a conserved retroviral RNA packaging element from Moloney Murine Leukemia Virus. | |||||||||
Map data | The final average of 38 subvolumes of two sets of two stem loop structures (CD2) of MoMuLV. | |||||||||
Sample |
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Keywords | cryo-ET / tomography / retroviral RNA / MoMuLV / Moloney Murine Leukemia Virus / double hairpin | |||||||||
Biological species | Moloney murine leukemia virus | |||||||||
Method | subtomogram averaging / cryo EM | |||||||||
Authors | Miyazaki Y / Irobalieva RN / Tolbert B / Smalls-Mantey A / Iyalla K / Loeliger K / DSouza V / Khant H / Schmid MF / Garcia E ...Miyazaki Y / Irobalieva RN / Tolbert B / Smalls-Mantey A / Iyalla K / Loeliger K / DSouza V / Khant H / Schmid MF / Garcia E / Telesnitsky A / Chiu W / Summers MF | |||||||||
Citation | Journal: J Mol Biol / Year: 2010 Title: Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography. Authors: Yasuyuki Miyazaki / Rossitza N Irobalieva / Blanton S Tolbert / Adjoa Smalls-Mantey / Kilali Iyalla / Kelsey Loeliger / Victoria D'Souza / Htet Khant / Michael F Schmid / Eric L Garcia / ...Authors: Yasuyuki Miyazaki / Rossitza N Irobalieva / Blanton S Tolbert / Adjoa Smalls-Mantey / Kilali Iyalla / Kelsey Loeliger / Victoria D'Souza / Htet Khant / Michael F Schmid / Eric L Garcia / Alice Telesnitsky / Wah Chiu / Michael F Summers / Abstract: The 5'-untranslated regions of all gammaretroviruses contain a conserved "double-hairpin motif" (Ψ(CD)) that is required for genome packaging. Both hairpins (SL-C and SL-D) contain GACG tetraloops ...The 5'-untranslated regions of all gammaretroviruses contain a conserved "double-hairpin motif" (Ψ(CD)) that is required for genome packaging. Both hairpins (SL-C and SL-D) contain GACG tetraloops that, in isolated RNAs, are capable of forming "kissing" interactions stabilized by two intermolecular G-C base pairs. We have determined the three-dimensional structure of the double hairpin from the Moloney murine leukemia virus ([Ψ(CD)](2), 132 nt, 42.8 kDa) using a (2)H-edited NMR-spectroscopy-based approach. This approach enabled the detection of (1)H-(1)H dipolar interactions that were not observed in previous studies of isolated SL-C and SL-D hairpin RNAs using traditional (1)H-(1)H correlated and (1)H-(13)C-edited NMR methods. The hairpins participate in intermolecular cross-kissing interactions (SL-C to SL-D' and SLC' to SL-D) and stack in an end-to-end manner (SL-C to SL-D and SL-C' to SL-D') that gives rise to an elongated overall shape (ca 95 Å×45 Å×25 Å). The global structure was confirmed by cryo-electron tomography (cryo-ET), making [Ψ(CD)](2) simultaneously the smallest RNA to be structurally characterized to date by cryo-ET and among the largest to be determined by NMR. Our findings suggest that, in addition to promoting dimerization, [Ψ(CD)](2) functions as a scaffold that helps initiate virus assembly by exposing a cluster of conserved UCUG elements for binding to the cognate nucleocapsid domains of assembling viral Gag proteins. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1806.map.gz | 939.6 KB | EMDB map data format | |
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Header (meta data) | emd-1806-v30.xml emd-1806.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | 1806.png | 47.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1806 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1806 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1806.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The final average of 38 subvolumes of two sets of two stem loop structures (CD2) of MoMuLV. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.487 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : MLV Tandem Hairpin RNA
Entire | Name: MLV Tandem Hairpin RNA |
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Components |
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-Supramolecule #1000: MLV Tandem Hairpin RNA
Supramolecule | Name: MLV Tandem Hairpin RNA / type: sample / ID: 1000 Details: RNA synthesized by in vitro transcription and purified by polyacrylamide gel electrophoresis. Sequence of the RNA confirmed by NMR. Oligomeric state: Homodimer / Number unique components: 1 |
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Molecular weight | Theoretical: 42.8 KDa / Method: Not determined but identity confirmed by NMR |
-Macromolecule #1: MLV Tandem Hairpin RNA
Macromolecule | Name: MLV Tandem Hairpin RNA / type: rna / ID: 1 / Name.synonym: MLV Tandem Hairpin RNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: Moloney murine leukemia virus / synonym: Moloney Murine Leukemia Virus |
Molecular weight | Theoretical: 42.8 KDa |
Sequence | String: GGCGGACCCG UGGUGGAACA GACGUGUUCG GAACACCCGG CCGCAACCCU GGGAGACGUC CCAGGG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
-Sample preparation
Concentration | 1.03 mg/mL |
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Buffer | pH: 7 Details: Tris buffer, pH 7.0, containing 140 mM KCl and 2 mM MgCl2 |
Grid | Details: 200 mesh gold grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: Vitrobot Mark III / Method: 1 blot, 1 second |
-Electron microscopy
Microscope | JEOL 2200FSC |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 23123 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal magnification: 20000 |
Specialist optics | Energy filter - Name: In column Omega-type filter |
Sample stage | Specimen holder: Gatan 70 degree holder / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Temperature | Min: 98 K / Max: 98 K / Average: 98 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Average electron dose: 85 e/Å2 |
-Image processing
Final reconstruction | Algorithm: OTHER / Software - Name: IMOD / Details: Final map was an average of 38 subvolumes. |
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Details | Tomogram was reconstructed using IMOD. Average number of tilts used in the 3D reconstructions: 60. Average tomographic tilt angle increment: 2. |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera, X-plor |
Details | Protocol: Distance geometry refinement with the Cyana software package using NMR-derived restraints. The cryo-ET data were not employed as refinement restraints. The determined NMR structure (2LIF) was fitted into the cryo-ET density map using Chimera and X-plor. |
Refinement | Space: REAL Target criteria: Lowest target functions, equals sum of the square of the distance and angle restraint violations |