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- EMDB-5639: Cryo-electron tomography reconstruction of native HIV-1 core -

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Basic information

Entry
Database: EMDB / ID: EMD-5639
TitleCryo-electron tomography reconstruction of native HIV-1 core
Map dataThe figure shows the simulated density of all-atom HIV-1 capsid model (3J3Y) overlaid with a slice of HIV-1 core tomogram.
Sample
  • Sample: HIV-1 core with A14C/E45C cross-linked capsid protein
  • Virus: Human immunodeficiency virus 1
Keywordscryo-electron tomography / HIV-1 core
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / virion membrane / structural molecule activity / RNA binding / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / 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 ...Gag protein p6 / Gag protein p6 / : / 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 finger / 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
Methodelectron tomography / cryo EM
AuthorsZhao G / Perilla JR / Yufenyuy E / Meng X / Chen B / Ning J / Ahn J / Gronenborn AM / Schulten K / Aiken C / Zhang P
CitationJournal: Nature / Year: 2013
Title: Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
Authors: Gongpu Zhao / Juan R Perilla / Ernest L Yufenyuy / Xin Meng / Bo Chen / Jiying Ning / Jinwoo Ahn / Angela M Gronenborn / Klaus Schulten / Christopher Aiken / Peijun Zhang /
Abstract: Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, ...Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.
History
DepositionApr 12, 2013-
Header (metadata) releaseMay 29, 2013-
Map releaseMay 29, 2013-
UpdateJun 12, 2013-
Current statusJun 12, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.355
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.355
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j3y
  • Surface level: 0.355
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j3q
  • Surface level: 0.355
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j3q
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5639_1.jpg

emd_5639_2.jpg

Downloads & links

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Map

FileDownload / File: emd_5639.map.gz / Format: CCP4 / Size: 17.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe figure shows the simulated density of all-atom HIV-1 capsid model (3J3Y) overlaid with a slice of HIV-1 core tomogram.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.25 Å/pix.
x 161 pix.
= 1006.25 Å		6.25 Å/pix.
x 175 pix.
= 1093.75 Å		6.25 Å/pix.
x 163 pix.
= 1018.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 6.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.355 / Movie #1: 0.355
Minimum - Maximum0.0 - 0.62596595
Average (Standard dev.)0.06133261 (±0.12504502)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions175163161
Spacing175163161
CellA: 1018.75 Å / B: 1093.75 Å / C: 1006.25 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.256.256.25
M x/y/z163175161
origin x/y/z0.0000.0000.000
length x/y/z1018.7501093.7501006.250
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS163175161
D min/max/mean0.0000.6260.061

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Supplemental data

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Sample components

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Entire : HIV-1 core with A14C/E45C cross-linked capsid protein

EntireName: HIV-1 core with A14C/E45C cross-linked capsid protein
Components
  • Sample: HIV-1 core with A14C/E45C cross-linked capsid protein
  • Virus: Human immunodeficiency virus 1

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Supramolecule #1000: HIV-1 core with A14C/E45C cross-linked capsid protein

SupramoleculeName: HIV-1 core with A14C/E45C cross-linked capsid protein / type: sample / ID: 1000 / Details: The sample was purified from HIV-1 virions / Number unique components: 1

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Name.synonym: HIV-1
Details: HIV-1 core was isolated from virions carrying A14C/E45C mutation in capsid protein.
NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Sci species strain: R9 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: HIV-1
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration0.011 mg/mL
BufferpH: 8 / Details: 10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA
GridDetails: Quantifoil R2/2 200 mesh holey carbon copper grids
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER
Method: Purified HIV-1 A14C/E45C cores (3 uL) were applied to the carbon side of glow-discharged, perforated R2/2 Quantifoil grids and quickly mixed with 3 uL of a 15 nM fiducial gold bead solution ...Method: Purified HIV-1 A14C/E45C cores (3 uL) were applied to the carbon side of glow-discharged, perforated R2/2 Quantifoil grids and quickly mixed with 3 uL of a 15 nM fiducial gold bead solution before plunge-freezing.

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80 K / Max: 85 K / Average: 82 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 115,000 times magnification
DateSep 11, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 53 / Average electron dose: 120 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 39000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 66 ° / Tilt series - Axis1 - Angle increment: 2 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: tomo3d
Details: The raw tomogram was denoised using the nonlinear anisotropic diffusion edge-enhancing algorithm available in IMOD. The core density was segmented out using Volume Tracer in UCSF Chimera.
Number images used: 53

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Atomic model buiding 1

Initial modelPDB ID:

3j34

SoftwareName: MD
DetailsThe model was built using hexamer of hexamers (PDB entry 3J34) and pentamer of hexamers (computer-based MD model available upon request).
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j3q:
Atomic-level structure of the entire HIV-1 capsid

PDB-3j3y:
Atomic-level structure of the entire HIV-1 capsid (186 hexamers + 12 pentamers)

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