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- EMDB-8986: A 3.1 Angstrom sub-tomogram average of HIV-1 CA-SP1. -

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Basic information

Entry
Database: EMDB / ID: EMD-8986
TitleA 3.1 Angstrom sub-tomogram average of HIV-1 CA-SP1.
Map dataMap with a B-factor of 150 applied, as used in generating figures.
Sample
  • Virus: HIV-1 CA-SP1
Methodsubtomogram averaging / cryo EM / Resolution: 3.1 Å
AuthorsHimes BA / Zhang P
CitationJournal: Nat Methods / Year: 2018
Title: emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging.
Authors: Benjamin A Himes / Peijun Zhang /
Abstract: Macromolecular complexes are intrinsically flexible and often challenging to purify for structure determination by single-particle cryo-electron microscopy (cryo-EM). Such complexes can be studied by ...Macromolecular complexes are intrinsically flexible and often challenging to purify for structure determination by single-particle cryo-electron microscopy (cryo-EM). Such complexes can be studied by cryo-electron tomography (cryo-ET) combined with subtomogram alignment and classification, which in exceptional cases achieves subnanometer resolution, yielding insight into structure-function relationships. However, it remains challenging to apply this approach to specimens that exhibit conformational or compositional heterogeneity or are present in low abundance. To address this, we developed emClarity ( https://github.com/bHimes/emClarity/wiki ), a GPU-accelerated image-processing package featuring an iterative tomographic tilt-series refinement algorithm that uses subtomograms as fiducial markers and a 3D-sampling-function-compensated, multi-scale principal component analysis classification method. We demonstrate that our approach offers substantial improvement in the resolution of maps and in the separation of different functional states of macromolecular complexes compared with current state-of-the-art software.
History
DepositionJul 22, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseOct 31, 2018-
UpdateMar 27, 2019-
Current statusMar 27, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.993267486
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8986.png

Downloads & links

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Map

FileDownload / File: emd_8986.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap with a B-factor of 150 applied, as used in generating figures.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.4 / Movie #1: 0.9932675
Minimum - Maximum-8.348758999999999 - 14.062434
Average (Standard dev.)0.013832731 (±0.6134586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-8.34914.0620.014

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Supplemental data

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Sample components

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Entire : HIV-1 CA-SP1

EntireName: HIV-1 CA-SP1
Components
  • Virus: HIV-1 CA-SP1

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Supramolecule #1: HIV-1 CA-SP1

SupramoleculeName: HIV-1 CA-SP1 / type: virus / ID: 1 / Parent: 0 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
DetailsPlease refer to EMD-3782/ EMPIAR-10164

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsPlease refer to EMD-3782/ EMPIAR-10164
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.4 e/Å2 / Details: Please refer to EMD-3782/ EMPIAR-10164
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsPlease refer to EMD-3782/ EMPIAR-10164
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: emClarity (ver. 1.0.0) / Details: using emClarity 1.0.0 / Number subtomograms used: 162215
ExtractionNumber tomograms: 40 / Number images used: 199531 / Reference model: EMD-403 / Method: template matching
Details: template matching in emClarity, limited to 4nm resolution. using emClarity 1.0.0
CTF correctionDetails: "3D-CTF" (defocus gradient corrected back-projection) using emClarity 1.0.0
Final 3D classificationNumber classes: 1
Final angle assignmentType: OTHER / Details: Missing wedge compensated cross-correlation.
FSC plot (resolution estimation)

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