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- EMDB-52724: cryoEM structure of HIV-1 KAKA/G225R mature CA hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-52724
TitlecryoEM structure of HIV-1 KAKA/G225R mature CA hexamer
Map data
Sample
  • Complex: HIV-1 KAKA/G225R CA hexamer expressed and isolated from E.coli system
    • Protein or peptide: HIV-1 KAKA/G225R CA hexamer
KeywordsHIV-1 / KAKA/G225R / VIRUS
Biological speciesHIV-1 06TG.HT008 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsZhu Y / Shen J / Shen Y / Xu J / Zhang P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: bioRxiv / Year: 2025
Title: Structural basis for HIV-1 capsid adaption to rescue IP6-packaging deficiency.
Authors: Yanan Zhu / Alex B Kleinpeter / Juan S Rey / Juan Shen / Yao Shen / Jialu Xu / Nathan Hardenbrook / Long Chen / Anka Lucic / Juan R Perilla / Eric O Freed / Peijun Zhang /
Abstract: Inositol hexakisphosphate (IP6) promotes HIV-1 assembly via its interaction with the immature Gag lattice, effectively enriching IP6 within virions. During particle maturation, the HIV-1 protease ...Inositol hexakisphosphate (IP6) promotes HIV-1 assembly via its interaction with the immature Gag lattice, effectively enriching IP6 within virions. During particle maturation, the HIV-1 protease cleaves the Gag polyproteins comprising the immature Gag lattice, releasing IP6 from its original binding site and liberating the capsid (CA) domain of Gag. IP6 then promotes the assembly of mature CA protein into the capsid shell of the viral core, which is required for infection of new target cells. Recently, we reported HIV-1 Gag mutants that assemble virions independently of IP6. However, these mutants are non-infectious and unable to assemble stable capsids. Here, we identified a mutation in the C-terminus of CA - G225R - that restores capsid formation and infectivity to these IP6-packaging-deficient mutants. Furthermore, we show that G225R facilitates the assembly of purified CA into capsid-like particles (CLPs) at IP6 concentrations well below those required for WT CLP assembly. Using single-particle cryoEM, we solved structures of CA hexamer and hexameric lattice of mature CLPs harbouring the G225R mutation assembled in low-IP6 conditions. The high-resolution (2.7 Å) cryoEM structure combined with molecular dynamics simulations of the G225R capsid revealed that the otherwise flexible and disordered C-terminus of CA becomes structured, extending to the pseudo two-fold hexamer-hexamer interface, thereby stabilizing the mature capsid. This work uncovers a structural mechanism by which HIV-1 adapts to a deficiency in IP6 packaging. Furthermore, the ability of G225R to promote mature capsid assembly in low-IP6 conditions provides a valuable tool for capsid-related studies and may indicate a heretofore unknown role for the unstructured C-terminus in HIV-1 capsid assembly.
History
DepositionFeb 5, 2025-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52724.png

Downloads & links

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Map

FileDownload / File: emd_52724.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 256 pix.
= 171.52 Å		0.67 Å/pix.
x 256 pix.
= 171.52 Å		0.67 Å/pix.
x 256 pix.
= 171.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.169
Minimum - Maximum-0.0015540579 - 1.8753413
Average (Standard dev.)0.005513912 (±0.0537417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 171.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52724_msk_1.map
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Half map: #1

Fileemd_52724_half_map_1.map
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Half map: #2

Fileemd_52724_half_map_2.map
Projections & Slices
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Sample components

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Entire : HIV-1 KAKA/G225R CA hexamer expressed and isolated from E.coli system

EntireName: HIV-1 KAKA/G225R CA hexamer expressed and isolated from E.coli system
Components
  • Complex: HIV-1 KAKA/G225R CA hexamer expressed and isolated from E.coli system
    • Protein or peptide: HIV-1 KAKA/G225R CA hexamer

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Supramolecule #1: HIV-1 KAKA/G225R CA hexamer expressed and isolated from E.coli system

SupramoleculeName: HIV-1 KAKA/G225R CA hexamer expressed and isolated from E.coli system
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: HIV-1 06TG.HT008 (virus)

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Macromolecule #1: HIV-1 KAKA/G225R CA hexamer

MacromoleculeName: HIV-1 KAKA/G225R CA hexamer / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: HIV-1 06TG.HT008 (virus)
Molecular weightTheoretical: 25.614365 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPAE P FRDYVDRF ...String:
PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPAE P FRDYVDRF YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPG ATLEEMMTAC QGVGGPRHAA RVL

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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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8443 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1646193
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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