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- EMDB-3465: The structure of the mature HIV-1 CA hexamer in intact virus particles -

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Basic information

Entry
Database: EMDB / ID: EMD-3465
TitleThe structure of the mature HIV-1 CA hexamer in intact virus particles
Map dataCryo-electron tomography reconstruction of the mature CA hexameric lattice determined within intact HIV-1 viral particles
Sample
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: Capsid protein p24
Keywordsretrovirus / HIV-1 / capsid / hexamer / Viral protein
Function / homology
Function and homology information


viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
: / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...: / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 6.8 Å
AuthorsMattei S / Glass B
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research FoundationBR 3635/2-1 Germany
German Research FoundationKR 906/7-1 Germany
CitationJournal: Science / Year: 2016
Title: The structure and flexibility of conical HIV-1 capsids determined within intact virions.
Authors: Simone Mattei / Bärbel Glass / Wim J H Hagen / Hans-Georg Kräusslich / John A G Briggs /
Abstract: HIV-1 contains a cone-shaped capsid encasing the viral genome. This capsid is thought to follow fullerene geometry-a curved hexameric lattice of the capsid protein, CA, closed by incorporating 12 CA ...HIV-1 contains a cone-shaped capsid encasing the viral genome. This capsid is thought to follow fullerene geometry-a curved hexameric lattice of the capsid protein, CA, closed by incorporating 12 CA pentamers. Current models for core structure are based on crystallography of hexameric and cross-linked pentameric CA, electron microscopy of tubular CA arrays, and simulations. Here, we report subnanometer-resolution cryo-electron tomography structures of hexameric and pentameric CA within intact HIV-1 particles. Whereas the hexamer structure is compatible with crystallography studies, the pentamer forms using different interfaces. Determining multiple structures revealed how CA flexes to form the variably curved core shell. We show that HIV-1 CA assembles both aberrant and perfect fullerene cones, supporting models in which conical cores assemble de novo after maturation.
History
DepositionNov 10, 2016-
Header (metadata) releaseDec 28, 2016-
Map releaseDec 28, 2016-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5mcx
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3465.png

Downloads & links

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Map

FileDownload / File: emd_3465.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomography reconstruction of the mature CA hexameric lattice determined within intact HIV-1 viral particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 160 pix.
= 284.8 Å		1.78 Å/pix.
x 160 pix.
= 284.8 Å		1.78 Å/pix.
x 160 pix.
= 284.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16 / Movie #1: 0.16
Minimum - Maximum-0.19398293 - 0.61527306
Average (Standard dev.)0.00065499975 (±0.045561496)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 284.8 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1940.6150.001

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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
Components
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: Capsid protein p24

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: HIV-1 particles were produced by infection of MT-4 cells with HIV-1 strain NL43 by coculture.
NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Capsid protein p24

MacromoleculeName: Capsid protein p24 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 24.654268 KDa
SequenceString: PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF ...String:
PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPG ATLEEMMTAC QGV

UniProtKB: Gag polyprotein

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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: 7.4 / Component - Name: PBS
GridModel: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 292 K / Instrument: FEI VITROBOT MARK II
Details: 10nm colloidal gold was added to the sample prior to plunge freezing.
DetailsViral particles were purified from cell culture supernatant by iodixanol gradient centrifugation.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
DetailsNanoprobe
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsFrames were aligned using MotionCorr. Tilts in a tilt series were exposure filtered for cumulative electron dose. Tomograms were reconstructed using IMOD.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: AV3, TOM Toolbox) / Number subtomograms used: 72836
ExtractionNumber tomograms: 103 / Number images used: 652618 / Reference model: reference free
Details: Subtomograms were extracted along the manually rendered core surface of each viral particle.
Final angle assignmentType: OTHER / Software: (Name: AV3, TOM Toolbox) / Details: Cross-correlation based template matching.

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Atomic model buiding 1

Initial model
PDB IDChain

3h4e

chain_id: A, residue_range: 1-13, source_name: PDB, initial_model_type: experimental model

4xfx

chain_id: A, residue_range: 14-221, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-5mcx:
The structure of the mature HIV-1 CA hexamer in intact virus particles

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