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- EMDB-1518: Cryoelectron tomography of HIV-1 envelope spikes -

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Basic information

Entry
Database: EMDB / ID: EMD-1518
TitleCryoelectron tomography of HIV-1 envelope spikes
Map dataRaw tomogram of HIV-1 BaL virions, no filter applied.
Sample
  • Sample: HIV-1 BaL / SUPT1-CCR5 CL.30, provided by the AIDS Vaccine Program, SAIC Frederick, Inc., NCI, Frederick, MD. Lot p3955.
  • Virus: Human immunodeficiency virus 1
KeywordsHIV-1 / envelope spikes / cryo electron tomography
Biological speciesHuman immunodeficiency virus 1
Methodelectron tomography / cryo EM
AuthorsZhu P / Winkler H / Chertova E / Taylor KA / Roux KH
CitationJournal: PLoS Pathog / Year: 2008
Title: Cryoelectron tomography of HIV-1 envelope spikes: further evidence for tripod-like legs.
Authors: Ping Zhu / Hanspeter Winkler / Elena Chertova / Kenneth A Taylor / Kenneth H Roux /
Abstract: A detailed understanding of the morphology of the HIV-1 envelope (Env) spike is key to understanding viral pathogenesis and for informed vaccine design. We have previously presented a cryoelectron ...A detailed understanding of the morphology of the HIV-1 envelope (Env) spike is key to understanding viral pathogenesis and for informed vaccine design. We have previously presented a cryoelectron microscopic tomogram (cryoET) of the Env spikes on SIV virions. Several structural features were noted in the gp120 head and gp41 stalk regions. Perhaps most notable was the presence of three splayed legs projecting obliquely from the base of the spike head toward the viral membrane. Subsequently, a second 3D image of SIV spikes, also obtained by cryoET, was published by another group which featured a compact vertical stalk. We now report the cryoET analysis of HIV-1 virion-associated Env spikes using enhanced analytical cryoET procedures. More than 2,000 Env spike volumes were initially selected, aligned, and sorted into structural classes using algorithms that compensate for the "missing wedge" and do not impose any symmetry. The results show varying morphologies between structural classes: some classes showed trimers in the head domains; nearly all showed two or three legs, though unambiguous three-fold symmetry was not observed either in the heads or the legs. Subsequently, clearer evidence of trimeric head domains and three splayed legs emerged when head and leg volumes were independently aligned and classified. These data show that HIV-1, like SIV, also displays the tripod-like leg configuration, and, unexpectedly, shows considerable gp41 leg flexibility/heteromorphology. The tripod-like model for gp41 is consistent with, and helps explain, many of the unique biophysical and immunological features of this region.
History
DepositionJun 4, 2008-
Header (metadata) releaseJun 10, 2008-
Map releaseMar 31, 2009-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

1518.gif

Downloads & links

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Map

FileDownload / File: emd_1518.map.gz / Format: CCP4 / Size: 154.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRaw tomogram of HIV-1 BaL virions, no filter applied.
Voxel sizeX=Y=Z: 5.56 Å
Density
Minimum - Maximum-266.497000000000014 - 306.098000000000013
Average (Standard dev.)2.07057 (±68.350499999999997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-113-880
Dimensions2271771
Spacing2271771
CellA: 984.12 Å / B: 1262.12 Å / C: 5.56 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.565.565.56
M x/y/z1772271
origin x/y/z0.0000.0000.000
length x/y/z984.1201262.1205.560
α/β/γ90.00090.00090.000
start NX/NY/NZ494949
NX/NY/NZ969696
MAP C/R/S123
start NC/NR/NS-88-1130
NC/NR/NS1772271
D min/max/mean-266.497306.0982.071

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Supplemental data

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Sample components

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Entire : HIV-1 BaL / SUPT1-CCR5 CL.30, provided by the AIDS Vaccine Progra...

EntireName: HIV-1 BaL / SUPT1-CCR5 CL.30, provided by the AIDS Vaccine Program, SAIC Frederick, Inc., NCI, Frederick, MD. Lot p3955.
Components
  • Sample: HIV-1 BaL / SUPT1-CCR5 CL.30, provided by the AIDS Vaccine Program, SAIC Frederick, Inc., NCI, Frederick, MD. Lot p3955.
  • Virus: Human immunodeficiency virus 1

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Supramolecule #1000: HIV-1 BaL / SUPT1-CCR5 CL.30, provided by the AIDS Vaccine Progra...

SupramoleculeName: HIV-1 BaL / SUPT1-CCR5 CL.30, provided by the AIDS Vaccine Program, SAIC Frederick, Inc., NCI, Frederick, MD. Lot p3955.
type: sample / ID: 1000
Details: The map is the raw tomogram of HIV-1 BaL virus. The envelope spikes (trimer of gp120 and ecto domain of gp41, total MW is about 0.45 MegaDaltons)on the virion surface were picked up and ...Details: The map is the raw tomogram of HIV-1 BaL virus. The envelope spikes (trimer of gp120 and ecto domain of gp41, total MW is about 0.45 MegaDaltons)on the virion surface were picked up and subject to 3D alignment and classification analysis.
Oligomeric state: Highly purified virus. The envelope spikes on the virion surface are trimer.
Number unique components: 1

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Name.synonym: HIV-1
Details: The envelope spikes are distributed on the surface of HIV-1 virions.
NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: HIV-1
Host (natural)Organism: Homo sapiens (human) / synonym: BACTERIA(EUBACTERIA)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography

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Sample preparation

Concentration2.8 mg/mL
BufferpH: 7.4 / Details: Originally in TNE, resuspend in PBS
GridDetails: 300 mesh R2/1 Quantifoil grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Home made. Vitrification carried out in cold room
Method: Blot for 5-6 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
TemperatureAverage: 97 K
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal magnification: 43200
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 57 ° / Tilt series - Axis1 - Angle increment: 2 °

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Image processing

DetailsThe tilt angles were determined using saxton schedule. The angle increment is 2 deg at low tilt angles range and decreased to about 1 deg at high tilt angles range.
Final reconstructionAlgorithm: OTHER / Software - Name: PROTOMO / Number images used: 84

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