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- EMDB-12287: HIV-1 Gag T8I NC-RNA layer -

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Basic information

Entry
Database: EMDB / ID: EMD-12287
TitleHIV-1 Gag T8I NC-RNA layer
Map data
Sample
  • Virus: Human immunodeficiency virus 1
Function / homology
Function and homology information


viral process / viral capsid / nucleic acid binding / zinc ion binding
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / 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
Methodsubtomogram averaging / cryo EM / Resolution: 15.1 Å
AuthorsMendonca L / Zhang P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust206422/Z/17/Z United Kingdom
CitationJournal: Commun Biol / Year: 2021
Title: CryoET structures of immature HIV Gag reveal six-helix bundle.
Authors: Luiza Mendonça / Dapeng Sun / Jiying Ning / Jiwei Liu / Abhay Kotecha / Mateusz Olek / Thomas Frosio / Xiaofeng Fu / Benjamin A Himes / Alex B Kleinpeter / Eric O Freed / Jing Zhou / ...Authors: Luiza Mendonça / Dapeng Sun / Jiying Ning / Jiwei Liu / Abhay Kotecha / Mateusz Olek / Thomas Frosio / Xiaofeng Fu / Benjamin A Himes / Alex B Kleinpeter / Eric O Freed / Jing Zhou / Christopher Aiken / Peijun Zhang /
Abstract: Gag is the HIV structural precursor protein which is cleaved by viral protease to produce mature infectious viruses. Gag is a polyprotein composed of MA (matrix), CA (capsid), SP1, NC (nucleocapsid), ...Gag is the HIV structural precursor protein which is cleaved by viral protease to produce mature infectious viruses. Gag is a polyprotein composed of MA (matrix), CA (capsid), SP1, NC (nucleocapsid), SP2 and p6 domains. SP1, together with the last eight residues of CA, have been hypothesized to form a six-helix bundle responsible for the higher-order multimerization of Gag necessary for HIV particle assembly. However, the structure of the complete six-helix bundle has been elusive. Here, we determined the structures of both Gag in vitro assemblies and Gag viral-like particles (VLPs) to 4.2 Å and 4.5 Å resolutions using cryo-electron tomography and subtomogram averaging by emClarity. A single amino acid mutation (T8I) in SP1 stabilizes the six-helix bundle, allowing to discern the entire CA-SP1 helix connecting to the NC domain. These structures provide a blueprint for future development of small molecule inhibitors that can lock SP1 in a stable helical conformation, interfere with virus maturation, and thus block HIV-1 infection.
History
DepositionFeb 1, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMar 23, 2022-
Current statusMar 23, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.82
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.82
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12287.png

Downloads & links

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Map

FileDownload / File: emd_12287.map.gz / Format: CCP4 / Size: 12.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.76 Å/pix.
x 147 pix.
= 405.72 Å		2.76 Å/pix.
x 147 pix.
= 405.72 Å		2.76 Å/pix.
x 147 pix.
= 405.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.82 / Movie #1: 1.82
Minimum - Maximum-2.1549156 - 14.339675
Average (Standard dev.)0.07742818 (±0.4983202)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions147147147
Spacing147147147
CellA=B=C: 405.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z147147147
origin x/y/z0.0000.0000.000
length x/y/z405.720405.720405.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS147147147
D min/max/mean-2.15514.3400.077

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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: STRAIN / 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
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 15.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 6747
ExtractionNumber tomograms: 90 / Number images used: 131942
Final 3D classificationNumber classes: 3 / Avg.num./class: 2000
Final angle assignmentType: OTHER

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