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Yorodumi- EMDB-7079: Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7079 | |||||||||||||||
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Title | Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach | |||||||||||||||
Map data | DIS dimer 3D map from data set 1 (JEOL2200FS microscope, DE12 detector) | |||||||||||||||
Sample | 30 kDa HIV-1 RNA Dimerization Signal != Human immunodeficiency virus 1 30 kDa HIV-1 RNA Dimerization Signal
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Biological species | Human immunodeficiency virus 1 | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 Å | |||||||||||||||
Authors | Zhang K / Keane S / Su Z / Case D / Ludtke S / Summers M / Chiu W | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Structure / Year: 2018 Title: Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach. Authors: Kaiming Zhang / Sarah C Keane / Zhaoming Su / Rossitza N Irobalieva / Muyuan Chen / Verna Van / Carly A Sciandra / Jan Marchant / Xiao Heng / Michael F Schmid / David A Case / Steven J ...Authors: Kaiming Zhang / Sarah C Keane / Zhaoming Su / Rossitza N Irobalieva / Muyuan Chen / Verna Van / Carly A Sciandra / Jan Marchant / Xiao Heng / Michael F Schmid / David A Case / Steven J Ludtke / Michael F Summers / Wah Chiu / Abstract: Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, ...Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS]; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs. | |||||||||||||||
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_7079.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-7079-v30.xml emd-7079.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_7079.png | 49 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7079 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7079 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7079.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | DIS dimer 3D map from data set 1 (JEOL2200FS microscope, DE12 detector) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.01 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 : 30 kDa HIV-1 RNA Dimerization Signal
Entire | Name: 30 kDa HIV-1 RNA Dimerization Signal |
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Components |
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-Supramolecule #1: Human immunodeficiency virus 1
Supramolecule | Name: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes |
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Host system | Organism: Human immunodeficiency virus 1 |
Molecular weight | Experimental: 30 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | HIV-1 RNA Dimerization Signal |
-Electron microscopy
Microscope | JEOL 2200FS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 25000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Number grids imaged: 4 / Number real images: 540 / Average electron dose: 75.0 e/Å2 |
-Image processing
CTF correction | Software - Name: EMAN2 (ver. 2.1) |
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Startup model | Type of model: OTHER Details: Starting model made from 2D class averages by EMAN2 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: EMAN2 (ver. 2.1) |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.1) / Number images used: 20366 |