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- EMDB-6439: Helical cryo-EM reconstruction of HIV Rev filament -

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Basic information

Entry
Database: EMDB / ID: EMD-6439
TitleHelical cryo-EM reconstruction of HIV Rev filament
Map dataHelical Reconstruction of HIV-1 Rev filament
Sample
  • Sample: HIV-1 Rev filament
  • Protein or peptide: Rev protein
KeywordsHIV 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
Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein)
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
Methodhelical reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsDiMattia MA / Watts NR / Cheng N / Huang R / Heymann JB / Wingfield PT / Grimes JM / Stuart DI / Steven AC
CitationJournal: 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
DepositionAug 25, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseJun 22, 2016-
UpdateJul 20, 2016-
Current statusJul 20, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6439.gif

Downloads & links

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Map

FileDownload / File: emd_6439.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical Reconstruction of HIV-1 Rev filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 300 pix.
= 304.65 Å		1.02 Å/pix.
x 300 pix.
= 304.65 Å		1.02 Å/pix.
x 300 pix.
= 304.65 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0155 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.6 / Movie #1: 1.6
Minimum - Maximum-5.7130022 - 7.22380447
Average (Standard dev.)0.0 (±0.80485672)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-149-150
Dimensions300300300
Spacing300300300
CellA=B=C: 304.65 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.01551.01551.0155
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z304.650304.650304.650
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-149-150-150
NC/NR/NS300300300
D min/max/mean-5.7137.2240.000

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Supplemental data

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Sample components

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Entire : HIV-1 Rev filament

EntireName: HIV-1 Rev filament
Components
  • Sample: HIV-1 Rev filament
  • Protein or peptide: Rev protein

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Supramolecule #1000: HIV-1 Rev filament

SupramoleculeName: 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

MacromoleculeName: Rev protein / type: protein_or_peptide / ID: 1 / Oligomeric state: helical polymer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / synonym: HIV-1
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Protein Rev

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration2.0 mg/mL
GridDetails: C-flat holey carbon grids
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI POLARA 300
DateFeb 19, 2015
Image recordingCategory: 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.09 µm / Nominal defocus min: 0.99 µm / Nominal magnification: 20000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsThe particles were aligned using IHRSR.
Final reconstructionApplied 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 correctionDetails: Each particle

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