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- EMDB-1596: HIV-1 Env spike maps using various alignment and classfication co... -

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Basic information

Entry
Database: EMDB / ID: EMD-1596
TitleHIV-1 Env spike maps using various alignment and classfication combinations
Map dataClassified HIV-1 Env spikes using different alignment and classification strategies.
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 spike
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / 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
DepositionJan 27, 2009-
Header (metadata) releaseFeb 3, 2009-
Map releaseApr 1, 2009-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1596.gif

Schematic.jpg

Downloads & links

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Map

FileDownload / File: emd_1596.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClassified HIV-1 Env spikes using different alignment and classification strategies.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.56 Å/pix.
x 64 pix.
= 355.84 Å		5.56 Å/pix.
x 64 pix.
= 355.84 Å		5.56 Å/pix.
x 64 pix.
= 355.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.36 / Movie #1: 0.4
Minimum - Maximum-1.12955 - 1.39125
Average (Standard dev.)-0.00000000142318 (±0.232462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-31-32-32
Dimensions646464
Spacing646464
CellA=B=C: 355.84 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.565.565.56
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z355.840355.840355.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS-32-31-32
NC/NR/NS646464
D min/max/mean-1.1301.391-0.000

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Supplemental data

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Others

Details[readme.txt]
Reference:
Zhu P, Winkler H, Chertova E, Taylor KA, Roux KH (2008) Cryoelectron Tomography of HIV-1
Envelope Spikes: Further Evidence for Tripod-Like Legs. PLoS Pathog 4(11): e1000203.

The folders in 1596_class_maps.zip consist of aligned and classified HIV-1 Env spikes maps using various alignment
and classification combinations as shown in figure 3 of the reference. Please refer back to
the reference for details.

A_WW: Panel A
Aligned: whole, Classified: whole
B_WH: Panel B
Aligned: whole, Classified: head
C_WL: Panel C
Aligned: whole, Classified: legs
D_HH: Panel D
Aligned: head, Classified: head
E_LL: Panel E
Aligned: legs, Classified: legs

In each subfolder,
*-cls-[1-8].map: eight classes produced for each combination

Image

File: Schematic.jpg
File1596_class_maps.zip (36.4 MB)

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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 envelope spikes are distributed on the surface of HIV-1 virions.
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 BaL SUPT1-CCR5 CL.30
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 BaL SUPT1-CCR5 CL.30
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

Concentration2.8 mg/mL
BufferpH: 7.4 / Details: Originally in TNE, resuspend in PBS
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal magnification: 43200
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingAverage electron dose: 1.5 e/Å2

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Image processing

Final reconstructionSoftware - Name: Protomo

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