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- EMDB-10207: A 4.2 Angstrom structure of HIV-1 CA-SP1 -

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Basic information

Entry
Database: EMDB / ID: EMD-10207
TitleA 4.2 Angstrom structure of HIV-1 CA-SP1
Map dataA 4.2A structure of HIV-1 CA-SP1.
Sample
  • Virus: Human immunodeficiency virus 1
    • Other: Virus-like particle
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 4.2 Å
AuthorsTuronova B / Hagen WJH / Obr M / Mosalaganti S / Kraeusslich HG / Beck M
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council724349 Germany
CitationJournal: Nat Commun / Year: 2020
Title: Benchmarking tomographic acquisition schemes for high-resolution structural biology.
Authors: Beata Turoňová / Wim J H Hagen / Martin Obr / Shyamal Mosalaganti / J Wouter Beugelink / Christian E Zimmerli / Hans-Georg Kräusslich / Martin Beck /
Abstract: Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in ...Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines.
History
DepositionAug 8, 2019-
Header (metadata) releaseAug 28, 2019-
Map releaseFeb 26, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10207.png

Downloads & links

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Map

FileDownload / File: emd_10207.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA 4.2A structure of HIV-1 CA-SP1.
Voxel sizeX=Y=Z: 1.3269 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.50212526 - 0.55144703
Average (Standard dev.)0.0052128946 (±0.071204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 254.7648 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.32690104166671.32690104166671.3269010416667
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z254.765254.765254.765
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.5020.5510.005

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Supplemental data

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Additional map: A CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_1.map
AnnotationA CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained with the DS VPP def tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_10.map
AnnotationA CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained with the continuous tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A CTF-reweighted even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_11.map
AnnotationA CTF-reweighted even half-map of HIV-1 CA-SP1 obtained with the continuous tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_12.map
AnnotationA CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained with the bidirectional tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_13.map
AnnotationA CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained with the DS VPP def tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A CTF-reweighted even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_14.map
AnnotationA CTF-reweighted even half-map of HIV-1 CA-SP1 obtained with the DS VPP def tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: A CTF-reweighted map of HIV-1 CA-SP1 obtained with...

Fileemd_10207_additional_15.map
AnnotationA CTF-reweighted map of HIV-1 CA-SP1 obtained with the DS VPP def tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_16.map
AnnotationA CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained with the DS inc tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted map of HIV-1 CA-SP1 obtained with...

Fileemd_10207_additional_17.map
AnnotationA CTF-reweighted map of HIV-1 CA-SP1 obtained with the DS dec tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_18.map
AnnotationA CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained with the dose-symmetric tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_19.map
AnnotationA CTF-reweighted even half-map of HIV-1 CA-SP1 obtained with the dose-symmetric tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_2.map
AnnotationA CTF-reweighted even half-map of HIV-1 CA-SP1 obtained with the DS VPP def tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted map of HIV-1 CA-SP1 obtained with...

Fileemd_10207_additional_20.map
AnnotationA CTF-reweighted map of HIV-1 CA-SP1 obtained with the dose-symmetric tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_21.map
AnnotationA CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained with the continuous tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_22.map
AnnotationA CTF-reweighted even half-map of HIV-1 CA-SP1 obtained with the continuous tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_23.map
AnnotationA CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained with the bidirectional tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_24.map
AnnotationA CTF-reweighted even half-map of HIV-1 CA-SP1 obtained with the bidirectional tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted map of HIV-1 CA-SP1 obtained with...

Fileemd_10207_additional_25.map
AnnotationA CTF-reweighted map of HIV-1 CA-SP1 obtained with the bidirectional tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw map of HIV-1 CA-SP1 obtained with...

Fileemd_10207_additional_26.map
AnnotationA raw map of HIV-1 CA-SP1 obtained with the DS VPP foc tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_27.map
AnnotationA raw odd half-map of HIV-1 CA-SP1 obtained with the DS VPP def tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_28.map
AnnotationA raw even half-map of HIV-1 CA-SP1 obtained with the DS VPP def tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw map of HIV-1 CA-SP1 obtained with...

Fileemd_10207_additional_29.map
AnnotationA raw map of HIV-1 CA-SP1 obtained with the DS VPP def tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_3.map
AnnotationA CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained with the DS inc tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_30.map
AnnotationA raw odd half-map of HIV-1 CA-SP1 obtained with the DS inc tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_31.map
AnnotationA raw even half-map of HIV-1 CA-SP1 obtained with the DS inc tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw map of HIV-1 CA-SP1 obtained with...

Fileemd_10207_additional_32.map
AnnotationA raw map of HIV-1 CA-SP1 obtained with the DS inc tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_33.map
AnnotationA raw odd half-map of HIV-1 CA-SP1 obtained with the DS dec tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_34.map
AnnotationA raw even half-map of HIV-1 CA-SP1 obtained with the DS dec tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_35.map
AnnotationA CTF-reweighted even half-map of HIV-1 CA-SP1 obtained with the DS inc tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_36.map
AnnotationA raw even half-map of HIV-1 CA-SP1 obtained with the dose-symmetric tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw map of HIV-1 CA-SP1 obtained with...

Fileemd_10207_additional_37.map
AnnotationA raw map of HIV-1 CA-SP1 obtained with the continuous tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A raw map of HIV-1 CA-SP1 obtained with...

Fileemd_10207_additional_38.map
AnnotationA raw map of HIV-1 CA-SP1 obtained with the bidirectional tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted map of HIV-1 CA-SP1 obtained with...

Fileemd_10207_additional_39.map
AnnotationA CTF-reweighted map of HIV-1 CA-SP1 obtained with the continuous tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_4.map
AnnotationA CTF-reweighted even half-map of HIV-1 CA-SP1 obtained with the DS inc tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_5.map
AnnotationA CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained with the DS dec tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_6.map
AnnotationA CTF-reweighted even half-map of HIV-1 CA-SP1 obtained with the bidirectional tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_7.map
AnnotationA CTF-reweighted even half-map of HIV-1 CA-SP1 obtained with the DS dec tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_8.map
AnnotationA CTF-reweighted odd half-map of HIV-1 CA-SP1 obtained with the dose-symmetric tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: A CTF-reweighted even half-map of HIV-1 CA-SP1 obtained...

Fileemd_10207_additional_9.map
AnnotationA CTF-reweighted even half-map of HIV-1 CA-SP1 obtained with the dose-symmetric tilt-scheme using C6 symmetry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Virus: Human immunodeficiency virus 1
    • Other: Virus-like particle

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Virus-like particle

MacromoleculeName: Virus-like particle / type: other / ID: 1 / Classification: other
SequenceString:
Not applic able

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3708 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Average electron dose: 3.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 5 / Number images used: 199569
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4.1.8)CTF estimation
NOVACTFCTF correction

Details: 3D-CTF correction was performed using novaCTF with multiplication as a correction method, slab size of 15nm and astigmatism correction. Final map was CTF-reweighted.
Final angle assignmentType: OTHER / Details: Cross-correlation based template matching
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 15241
FSC plot (resolution estimation)

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