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Yorodumi- PDB-6bg9: HYBRID NMR/CRYO-EM STRUCTURE OF THE HIV-1 RNA DIMERIZATION SIGNAL -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bg9 | |||||||||
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Title | HYBRID NMR/CRYO-EM STRUCTURE OF THE HIV-1 RNA DIMERIZATION SIGNAL | |||||||||
Components | RNA dimerization signal | |||||||||
Keywords | RNA / RNA INERNAL LOOPS / SHEARED GA PAIRS / GU WOBBLE / S-TURN THERMODYNAMICS | |||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / SOLUTION NMR / subtomogram averaging / molecular dynamics / cryo EM / Resolution: 9 Å | |||||||||
Authors | Summers, M.F. | |||||||||
Funding support | United States, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6bg9.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6bg9.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6bg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/6bg9 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/6bg9 | HTTPS FTP |
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-Related structure data
Related structure data | 7080MC 7079C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 15359.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: in vitro transcription vector pT7-TP(deltai) (others) |
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-Experimental details
-Experiment
Experiment |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging | ||||||||||||||||||
NMR experiment |
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NMR details | Text: NMR studies conducted with multiple samples prepared by differential nucleotide-specific 2H labeling. |
-Sample preparation
Component | Name: Human immunodeficiency virus 1Subtypes of HIV / Type: ORGANELLE OR CELLULAR COMPONENT Details: RNA prepared by in vitro transcription using T7 RNA polymerase Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: in vitro transcription vector pT7-TP(deltai) (others) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details of virus | Isolate: OTHER / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details |
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Sample |
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Sample conditions | Details: Samples in D2O, 5 mM NaCl, 140 mM KCl, 1 mM MgCl2, Tris, pH 7.2, T= 308K Ionic strength: 150 mM / Ionic strength err: 10 / Label: All samples / pH: 7.1 pD / Pressure: 1 atm / Temperature: 308 K |
-Data collection
Microscopy | Model: JEOL 2200FS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 25000 X |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Electron dose: 75 e/Å2 / Film or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Num. of grids imaged: 4 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||
3D reconstruction | Resolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20366 / Symmetry type: POINT | |||||||||||||||||||||
EM volume selection | Num. of tomograms: 540 / Num. of volumes extracted: 20366 | |||||||||||||||||||||
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 6 Details: Used GB for solvent simulation, NOEs and EM data simultaneously as restraints | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 20 / Conformers submitted total number: 20 |