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- EMDB-52052: Cryo-EM Density Map of the Immature HIV-1 CA Hexamer of Wild Type -

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Basic information

Entry
Database: EMDB / ID: EMD-52052
TitleCryo-EM Density Map of the Immature HIV-1 CA Hexamer of Wild Type
Map data
SampleHuman immunodeficiency virus 1 (HIV-1) != Human immunodeficiency virus 1

Human immunodeficiency virus 1 (HIV-1)

  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: HIV-1 Capsid Protein
KeywordsCapsid protein Hexameric assembly Virus-like particle HIV Structural Biology / STRUCTURAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 4.9 Å
AuthorsChen L / Zhang P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust206422/Z/17/Z United Kingdom
CitationJournal: bioRxiv / Year: 2024
Title: Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity.
Authors: Long Chen / Yuta Hikichi / Juan S Rey / Caner Akil / Yanan Zhu / Hana Veler / Yao Shen / Juan R Perilla / Eric O Freed / Peijun Zhang
Abstract: HIV-1 assembly is initiated by the binding of Gag polyproteins to the inner leaflet of the plasma membrane, mediated by the myristylated matrix (MA) domain of Gag. Subsequent to membrane binding, Gag ...HIV-1 assembly is initiated by the binding of Gag polyproteins to the inner leaflet of the plasma membrane, mediated by the myristylated matrix (MA) domain of Gag. Subsequent to membrane binding, Gag oligomerizes and buds as an immature, non-infectious virus particle, which, upon cleavage of the Gag precursor by the viral protease, transforms into a mature, infectious virion. During maturation, the MA lattice underlying the viral membrane undergoes a structural rearrangement and the newly released capsid (CA) protein forms a mature capsid that encloses the viral genome. While it is well established that formation of the mature capsid is essential to particle infectivity, the functional role of MA structural maturation remains unclear. Here, we examine MA maturation of an MA triple mutant, L20K/E73K/A82T, which exhibits distinct biochemical behaviours. The L20K/E73K/A82T mutant is a revertant derived by propagating the L20K mutant, which exhibits reduced infectivity and increased association of the Gag polyprotein with membranes. L20K/E73K/A82T replicates similarly to wild type but retains the increased Gag membrane binding properties of L20K. L20K/E73K/A82T MA also sediments to high-density fractions in sucrose gradients after detergent treatment under conditions that fully solubilize WT MA, suggesting enhanced MA-MA interactions. Cryo-electron tomography with subtomogram averaging reveals that the immature MA lattice of L20K/E73K/A82T closely resembles the wild type. However, mature virions of the triple mutant lack a detectable MA lattice, in stark contrast to both the wild type and L20K mutant. All-atom molecular dynamics simulations suggest that this absence results from destabilized inter-trimer interactions in the mature L20K/E73K/A82T MA. Furthermore, introducing additional mutations designed to disrupt the mature MA lattice does not impair particle infectivity. These findings suggest that an ordered, membrane-associated mature MA lattice is not essential for HIV-1 infectivity, providing new insights into the structural plasticity of the matrix during maturation and its functional role in the viral lifecycle.
History
DepositionNov 11, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52052.png

Downloads & links

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Map

FileDownload / File: emd_52052.map.gz / Format: CCP4 / Size: 29.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 198 pix.
= 297. Å		1.5 Å/pix.
x 198 pix.
= 297. Å		1.5 Å/pix.
x 198 pix.
= 297. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0000061
Minimum - Maximum-0.000011313194 - 0.000018304409
Average (Standard dev.)0.00000016123543 (±0.000002427264)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions198198198
Spacing198198198
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52052_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52052_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human immunodeficiency virus 1 (HIV-1)

EntireName: Human immunodeficiency virus 1 (HIV-1)
Components
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: HIV-1 Capsid Protein

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: HIV-1 Capsid Protein

MacromoleculeName: HIV-1 Capsid Protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGARASVLSG GELDKWEKIR LRPGGKKQYK LKHIVWASRE LERFAVNPGL LETSEGCRQI LGQLQPSLQT GSEELRSLYN TIAVLYCVHQ RIDVKDTKEA LDKIEEEQNK SKKKAQQAAA DTGNNSQVSQ NYPIVQNLQG QMVHQAISPR TLNAWVKVVE EKAFSPEVIP ...String:
MGARASVLSG GELDKWEKIR LRPGGKKQYK LKHIVWASRE LERFAVNPGL LETSEGCRQI LGQLQPSLQT GSEELRSLYN TIAVLYCVHQ RIDVKDTKEA LDKIEEEQNK SKKKAQQAAA DTGNNSQVSQ NYPIVQNLQG QMVHQAISPR TLNAWVKVVE EKAFSPEVIP MFSALSEGAT PQDLNTMLNT VGGHQAAMQM LKETINEEAA EWDRLHPVHA GPIAPGQMRE PRGSDIAGTT STLQEQIGWM THNPPIPVGE IYKRWIILGL NKIVRMYSPT SILDIRQGPK EPFRDYVDRF YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPG ATLEEMMTAC QGVGGPGHKA RVLAEAMSQV TNPATIMIQK GNFRNQRKTV KCFNCGKEGH IAKNCRAPRK KGCWKCGKEG HQMKDCTERQ ANFLGKIWPS HKGRPGNFLQ SRPEPTAPPE ESFRFGEETT TPSQKQEPID KELYPLASLR SLFGSDPSSQ

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 30782
ExtractionNumber tomograms: 89 / Number images used: 30782
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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