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- EMDB-9733: A T=4 icosahedral structure of HIV-1 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-9733
TitleA T=4 icosahedral structure of HIV-1 capsid
Map data
Sample
  • Virus: Human immunodeficiency virus 1
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsHe MZ / Zhang ZQ / Jiang J / Zheng QB / Li SW / Gu Y
CitationJournal: Viruses / Year: 2018
Title: T = 4 Icosahedral HIV-1 Capsid As an Immunogenic Vector for HIV-1 V3 Loop Epitope Display.
Authors: Zhiqing Zhang / Maozhou He / Shimeng Bai / Feng Zhang / Jie Jiang / Qingbing Zheng / Shuangquan Gao / Xiaodong Yan / Shaowei Li / Ying Gu / Ningshao Xia /
Abstract: The HIV-1 mature capsid (CA) assumes an amorphous, fullerene conical configuration due to its high flexibility. How native CA self-assembles is still unclear despite having well-defined structures of ...The HIV-1 mature capsid (CA) assumes an amorphous, fullerene conical configuration due to its high flexibility. How native CA self-assembles is still unclear despite having well-defined structures of its pentamer and hexamer building blocks. Here we explored the self-assembly of an engineered capsid protein built through artificial disulfide bonding (CA N21C/A22C) and determined the structure of one fraction of the globular particles. CA N21C/A22C was found to self-assemble into particles in relatively high ionic solutions. These particles contained disulfide-bonding hexamers as determined via non-reducing SDS-PAGE, and exhibited two major components of 57.3 S and 80.5 S in the sedimentation velocity assay. Particles had a globular morphology, approximately 40 nm in diameter, in negative-staining TEM. Through cryo-EM 3-D reconstruction, we determined a novel T = 4 icosahedral structure of CA, comprising 12 pentamers and 30 hexamers at 25 Å resolution. We engineered the HIV-1 V3 loop to the CA particles, and found the resultant particles resembled the morphology of their parental particles in TEM, had a positive reaction with V3-specific neutralizing antibodies, and conferred neutralization immunogenicity in mice. Our results shed light on HIV CA assembly and provide a particulate CA for epitope display.
History
DepositionNov 27, 2018-
Header (metadata) releaseDec 19, 2018-
Map releaseDec 19, 2018-
UpdateDec 19, 2018-
Current statusDec 19, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01134
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01134
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9733.png

Downloads & links

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Map

FileDownload / File: emd_9733.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 450 pix.
= 507.6 Å		1.13 Å/pix.
x 450 pix.
= 507.6 Å		1.13 Å/pix.
x 450 pix.
= 507.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01134 / Movie #1: 0.01134
Minimum - Maximum-0.0038397918 - 0.01622217
Average (Standard dev.)0.0016785166 (±0.0033872116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-225-225-225
Dimensions450450450
Spacing450450450
CellA=B=C: 507.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z507.600507.600507.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-225-225-225
NC/NR/NS450450450
D min/max/mean-0.0040.0160.002

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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

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / 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 systemOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 722
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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