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- EMDB-3469: The structure of the mature HIV-1 CA hexameric lattice with curva... -

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Entry
Database: EMDB / ID: 3469
TitleThe structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=5, twist=0
SampleHuman immunodeficiency virus 1
SourceHuman immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Map dataThe structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=5, twist=0
Methodsubtomogram averaging, at 8.2 Å resolution
AuthorsMattei S / Glass B
CitationScience, 2016, 354, 1434-1437

Science, 2016, 354, 1434-1437 Yorodumi Papers
The structure and flexibility of conical HIV-1 capsids determined within intact virions.
Simone Mattei / Bärbel Glass / Wim J H Hagen / Hans-Georg Kräusslich / John A G Briggs

Validation ReportPDB-ID: 5md1

SummaryFull reportAbout validation report
DateDeposition: Nov 10, 2016 / Header (metadata) release: Dec 28, 2016 / Map release: Dec 28, 2016 / Last update: Aug 30, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.2
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5md1
  • Surface level: 0.2
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_3469.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
1.78 Å/pix.
= 284.8 Å
160 pix
1.78 Å/pix.
= 284.8 Å
160 pix
1.78 Å/pix.
= 284.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.78 Å
Density
Contour Level:0.2 (by author), 0.2 (movie #1):
Minimum - Maximum-0.35202694 - 0.5875936
Average (Standard dev.)0.00037163286 (0.050761305)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin000
Limit159159159
Spacing160160160
CellA=B=C: 284.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z284.800284.800284.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.3520.5880.000

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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: HIV-1 particles were produced by infection of MT-4 cells with HIV-1 strain NL43 by coculture.
Number of components: 3

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Component #1: virus, Human immunodeficiency virus 1

VirusName: Human immunodeficiency virus 1 / Class: VIRION
Details: HIV-1 particles were produced by infection of MT-4 cells with HIV-1 strain NL43 by coculture.
Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Source (natural)Host Species: Homo sapiens / human

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Component #2: protein, Capsid protein p24

ProteinName: Capsid protein p24 / Recombinant expression: No
MassTheoretical: 8.370568 kDa
SourceSpecies: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Strain: NL43

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Component #3: protein, Capsid protein p24

ProteinName: Capsid protein p24 / Recombinant expression: No
MassTheoretical: 16.301689 kDa
SourceSpecies: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Strain: NL43

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 292 K / Humidity: 100 %
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: 2.2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 6500 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -66 - 66 deg.
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
Details: Frames were aligned using MotionCorr. Tilts in a tilt series were exposure filtered for cumulative electron dose. Tomograms were reconstructed using IMOD.
3D reconstructionSoftware: AV3, TOM Toolbox
CTF correction: CTF correction was performed using the ctfphaseflip program in IMOD prior to backprojection.
Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The final reconstruction is obtained by averaging, without further alignment, subtomograms that were selected based on the local curvature of the hexameric lattice. This reconstruction has hexamer-hexamer curvature parameters: tilt=5, twist=0.
Euler angles: Cross-correlation based template matching.

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Atomic model buiding

Output model

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