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- EMDB-3782: A 3.4 Angstrom structure of HIV-1 CA-SP1 by 3D-CTF correction of ... -

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Basic information

Entry
Database: EMDB / ID: 3782
TitleA 3.4 Angstrom structure of HIV-1 CA-SP1 by 3D-CTF correction of cryo-electron tomograms
SampleHuman immunodeficiency virus 1
SourceHuman immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Map dataNone
Methodsubtomogram averaging, at 3.4 Å resolution
AuthorsTuronova B / Schur FKM / Wan W / Briggs JAG
CitationJ. Struct. Biol., 2017, 199, 187-195

J. Struct. Biol., 2017, 199, 187-195 Yorodumi Papers
Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å.
Beata Turoňová / Florian K M Schur / William Wan / John A G Briggs

DateDeposition: Jul 5, 2017 / Header (metadata) release: Jun 29, 2016 / Map release: Aug 2, 2017 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.275
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.275
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.275
  • Imaged by UCSF CHIMERA
  • Download
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Map

Fileemd_3782.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.35 Å/pix.
= 259.2 Å
192 pix
1.35 Å/pix.
= 259.2 Å
192 pix
1.35 Å/pix.
= 259.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.275 (by author), 0.275 (movie #1):
Minimum - Maximum-0.60958225 - 0.9421653
Average (Standard dev.)0.020314952 (0.10203436)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin000
Limit191191191
Spacing192192192
CellA=B=C: 259.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z259.200259.200259.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.6100.9420.020

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Supplemental data

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Sample components

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Entire Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Details: Virus-like particles were obtained by in vitro assembly of a truncated Gag construct (deltaMACANCSP2) in presence of the maturation inhibitor Bevirimat
Number of components: 1

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Component #1: virus, Human immunodeficiency virus 1

VirusName: Human immunodeficiency virus 1 / Class: VIRUS-LIKE PARTICLE
Details: Virus-like particles were obtained by in vitro assembly of a truncated Gag construct (deltaMACANCSP2) in presence of the maturation inhibitor Bevirimat
Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pET11C
Source (natural)Host Species: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 5 mg/ml
Buffer solution: Virus-like particles were assembled in the presence of nucleic acid (73mer oligonucleotide, 1:10 molar ratio oligonucleotide:protein).
pH: 8
Support filmat 20 mA
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 288 K / Humidity: 95 %
Details: 10nM colloidal gold was added to the sample prior to plunge freezing.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Nanoprobe
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3.4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 5000 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -60 - 60 deg.
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionDetails: Number of frames ranged from 8-10 Exposure time per tilt ranged from 0.8 to 1.0 seconds

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C6 (6 fold cyclic)
Details: Frames were aligned using MotionCorr. Tilts in a tilt series were exposure filtered for cumulative electron dose. Tomograms were reconstructed using IMOD.
3D reconstructionAlgorithm: BACK PROJECTION / Software: AV3, TOM Toolbox
CTF correction: 3D CTF-correction was performed using NOVACTF. Defocus step 15nm.
Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Cross-correlation based template matching

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