|Entry||Database: EMDB / ID: EMD-6439|
|Title||Helical cryo-EM reconstruction of HIV Rev filament|
|Sample||HIV-1 Rev filament:|
|Keywords||HIV Rev filament / helical assembly / HIV life cycle / viral RNA / nuclear export|
|Function / homology||Anti-repression trans-activator protein, REV protein / host cell nucleolus / mRNA transport / host cell cytoplasm / DNA-binding transcription factor activity / viral process / RNA binding / Protein Rev|
Function and homology information
|Biological species||Human immunodeficiency virus 1 (HIV-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.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_6439.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.0155 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire HIV-1 Rev filament
|Entire||Name: HIV-1 Rev filament / Number of components: 1 / Oligomeric State: polymerized filament of Rev dimers|
-Component #1: protein, Rev protein
|Protein||Name: Rev protein / Oligomeric Details: helical polymer / Recombinant expression: Yes|
|Source||Species: Human immunodeficiency virus 1 (HIV-1)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|External references||UniProt: Protein Rev|
|Specimen||Specimen state: Filament / Method: cryo EM|
|Helical parameters||Axial symmetry: C6 (6 fold cyclic) / Hand: LEFT HANDED / Delta z: 21.2 Å / Delta phi: 22.1 %deg;|
|Sample solution||Specimen conc.: 2 mg/mL|
|Support film||C-flat holey carbon grids|
|Vitrification||Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 100 K|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300 / Date: Feb 19, 2015|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 20000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 990 - 3090 nm|
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 93 |
Details: Every image is the average of 30 frames recorded by the direct electron detector.
|Processing||Method: helical reconstruction / Details: The particles were aligned using IHRSR.|
|3D reconstruction||Algorithm: Iterative helical real space reconstruction (IHRSR)|
Software: BSOFT / CTF correction: Each particle / Resolution: 8.3 Å / Resolution method: FSC 0.333, semi-independent
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