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- EMDB-8404: Single particle helical reconstruction of protease cleavage produ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8404
TitleSingle particle helical reconstruction of protease cleavage product from HIV-1 Gag VLPs
Map dataCA tube assembled from gag cleavage
Sample
  • Complex: Single particle helical reconstruction of protease cleavage product from HIV-1 Gag VLPs
Methodhelical reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsFu X / Zhang P
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM082251 United States
National Science Foundation (NSF, United States)DMR-1310687 United States
offer of the Director GrantS10OD019995 United States
CitationJournal: Nat Commun / Year: 2016
Title: In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway.
Authors: Jiying Ning / Gonca Erdemci-Tandogan / Ernest L Yufenyuy / Jef Wagner / Benjamin A Himes / Gongpu Zhao / Christopher Aiken / Roya Zandi / Peijun Zhang /
Abstract: HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. ...HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. There are two competing models for the process of forming the mature HIV-1 core: the disassembly and de novo reassembly model and the non-diffusional displacive model. To study the maturation pathway, we simulate HIV-1 maturation in vitro by digesting immature particles and assembled virus-like particles with recombinant HIV-1 protease and monitor the process with biochemical assays and cryoEM structural analysis in parallel. Processing of Gag in vitro is accurate and efficient and results in both soluble capsid protein and conical or tubular capsid assemblies, seemingly converted from immature Gag particles. Computer simulations further reveal probable assembly pathways of HIV-1 capsid formation. Combining the experimental data and computer simulations, our results suggest a sequential combination of both displacive and disassembly/reassembly processes for HIV-1 maturation.
History
DepositionOct 6, 2016-
Header (metadata) releaseOct 19, 2016-
Map releaseDec 21, 2016-
UpdateFeb 3, 2021-
Current statusFeb 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 23.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 23.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8404.png

Downloads & links

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Map

FileDownload / File: emd_8404.map.gz / Format: CCP4 / Size: 8.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCA tube assembled from gag cleavage
Voxel sizeX=Y=Z: 4.52 Å
Density
Contour LevelBy AUTHOR: 23.6 / Movie #1: 23.6
Minimum - Maximum0.47561646 - 38.192886
Average (Standard dev.)16.79996 (±4.2317686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions130130130
Spacing130130130
CellA=B=C: 587.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.524.524.52
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z587.600587.600587.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
D min/max/mean0.47638.19316.800

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Supplemental data

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Sample components

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Entire : Single particle helical reconstruction of protease cleavage produ...

EntireName: Single particle helical reconstruction of protease cleavage product from HIV-1 Gag VLPs
Components
  • Complex: Single particle helical reconstruction of protease cleavage product from HIV-1 Gag VLPs

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Supramolecule #1: Single particle helical reconstruction of protease cleavage produ...

SupramoleculeName: Single particle helical reconstruction of protease cleavage product from HIV-1 Gag VLPs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 6 / Component - Concentration: 50.0 mM / Component - Formula: NaAc / Component - Name: Sodium Acetate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER
Detailssample is resulted from HIV-1 protease cleavage of in vitro assembled Gag VLPs

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 9.0 µm / Calibrated defocus min: 8.0 µm / Calibrated magnification: 66262 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 50000
Specialist opticsSpherical aberration corrector: No / Chromatic aberration corrector: No / Energy filter - Name: No
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 15.0 µm / Number grids imaged: 1 / Number real images: 2 / Average exposure time: 1.0 sec. / Average electron dose: 10.0 e/Å2
Details: Image was collected by single exposure, not movie mode.
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 863 / Software - Name: EMAN (ver. 2.0)
CTF correctionSoftware - Name: CTFFIND3
Final angle assignmentType: NOT APPLICABLE / Software - Name: IHRSH (ver. 1.5)
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 6.33573 Å
Applied symmetry - Helical parameters - Δ&Phi: -129.20547 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IHRSH (ver. 1.5) / Number images used: 863
FSC plot (resolution estimation)

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