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- EMDB-52726: cryoEM structure of HIV-1 KAKA/G225R mature CA tri-hexamer in Class2 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-52726
TitlecryoEM structure of HIV-1 KAKA/G225R mature CA tri-hexamer in Class2
Map data
Sample
  • Complex: HIV-1 KAKA/G225R CA hexamer expressed and isolated from E.coli system
KeywordsHIV-1 / KAKA/G225R / VIRUS
Biological speciesuncultured virus (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.24 Å
AuthorsZhu Y / Shen J / Shen Y / Zhang P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for HIV-1 capsid adaption to a deficiency in IP6 packaging.
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 by stabilizing the immature Gag lattice and becomes enriched within virions, where it is required for mature capsid assembly. Previously, we ...Inositol hexakisphosphate (IP6) promotes HIV-1 assembly by stabilizing the immature Gag lattice and becomes enriched within virions, where it is required for mature capsid assembly. Previously, we identified Gag mutants that package little IP6 yet assemble particles, though they are non-infectious due to defective capsid formation. Here, we report a compensatory mutation, G225R, in the C-terminus of capsid protein (CA) that restores capsid assembly and infectivity in these IP6-deficient mutants. G225R also enhances in vitro assembly of CA into capsid-like particles at far lower IP6 concentrations than required for wild-type CA. CryoEM structures of G225R CA hexamers and lattices at 2.7 Å resolution reveal that the otherwise disordered C-terminus becomes structured, stabilizing hexamer-hexamer interfaces. Molecular dynamics simulations support this mechanism. These findings uncover how HIV-1 can adapt to IP6 deficiency and highlight a previously unrecognized structural role of the CA C-terminus, while offering tools for capsid-related studies.
History
DepositionFeb 5, 2025-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52726.png

Downloads & links

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Map

FileDownload / File: emd_52726.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 192 pix.
= 263.981 Å		1.37 Å/pix.
x 192 pix.
= 263.981 Å		1.37 Å/pix.
x 192 pix.
= 263.981 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3749 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.118
Minimum - Maximum-0.31639683 - 0.558373
Average (Standard dev.)0.0010974632 (±0.029026903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 263.9808 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52726_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_52726_half_map_1.map
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Half map: #1

Fileemd_52726_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

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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
Source (natural)Organism: uncultured virus (environmental samples)

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 309508
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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