+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6439 | |||||||||
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Title | Helical cryo-EM reconstruction of HIV Rev filament | |||||||||
Map data | Helical Reconstruction of HIV-1 Rev filament | |||||||||
Sample |
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Keywords | HIV Rev filament / helical assembly / HIV life cycle / viral RNA / nuclear export | |||||||||
Function / homology | Function and homology information protein localization to nucleoplasm / host cell nucleolus / mRNA transport / viral process / host cell cytoplasm / DNA-binding transcription factor activity / RNA binding Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 8.3 Å | |||||||||
Authors | DiMattia MA / Watts NR / Cheng N / Huang R / Heymann JB / Wingfield PT / Grimes JM / Stuart DI / Steven AC | |||||||||
Citation | Journal: Structure / Year: 2016 Title: The Structure of HIV-1 Rev Filaments Suggests a Bilateral Model for Rev-RRE Assembly. Authors: Michael A DiMattia / Norman R Watts / Naiqian Cheng / Rick Huang / J Bernard Heymann / Jonathan M Grimes / Paul T Wingfield / David I Stuart / Alasdair C Steven / Abstract: HIV-1 Rev protein mediates the nuclear export of viral RNA genomes. To do so, Rev oligomerizes cooperatively onto an RNA motif, the Rev response element (RRE), forming a complex that engages with the ...HIV-1 Rev protein mediates the nuclear export of viral RNA genomes. To do so, Rev oligomerizes cooperatively onto an RNA motif, the Rev response element (RRE), forming a complex that engages with the host nuclear export machinery. To better understand Rev oligomerization, we determined four crystal structures of Rev N-terminal domain dimers, which show that they can pivot about their dyad axis, giving crossing angles of 90° to 140°. In parallel, we performed cryoelectron microscopy of helical Rev filaments. Filaments vary from 11 to 15 nm in width, reflecting variations in dimer crossing angle. These structures contain additional density, indicating that C-terminal domains become partially ordered in the context of filaments. This conformational variability may be exploited in the assembly of RRE/Rev complexes. Our data also revealed a third interface between Revs, which offers an explanation for how the arrangement of Rev subunits adapts to the "A"-shaped architecture of the RRE in export-active complexes. | |||||||||
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_6439.map.gz | 92.5 MB | EMDB map data format | |
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Header (meta data) | emd-6439-v30.xml emd-6439.xml | 9 KB 9 KB | Display Display | EMDB header |
Images | 400_6439.gif 80_6439.gif | 61.1 KB 4.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6439 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6439 | HTTPS FTP |
-Validation report
Summary document | emd_6439_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_6439_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_6439_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6439 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6439 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6439.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Helical Reconstruction of HIV-1 Rev filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0155 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 : HIV-1 Rev filament
Entire | Name: HIV-1 Rev filament |
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Components |
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-Supramolecule #1000: HIV-1 Rev filament
Supramolecule | Name: HIV-1 Rev filament / type: sample / ID: 1000 / Oligomeric state: polymerized filament of Rev dimers / Number unique components: 1 |
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-Macromolecule #1: Rev protein
Macromolecule | Name: Rev protein / type: protein_or_peptide / ID: 1 / Oligomeric state: helical polymer / Recombinant expression: Yes |
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Source (natural) | Organism: Human immunodeficiency virus 1 / synonym: HIV-1 |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Protein Rev |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 2.0 mg/mL |
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Grid | Details: C-flat holey carbon grids |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Feb 19, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 93 / Average electron dose: 25 e/Å2 Details: Every image is the average of 30 frames recorded by the direct electron detector. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.09 µm / Nominal defocus min: 0.99 µm / Nominal magnification: 20000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | The particles were aligned using IHRSR. |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 21.2 Å Applied symmetry - Helical parameters - Δ&Phi: 22.1 ° Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: OTHER / Software - Name: BSOFT |
CTF correction | Details: Each particle |