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- PDB-30og: HIV-1 CA tri-hexamer interface -

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Basic information

Entry
Database: PDB / ID: 30og
TitleHIV-1 CA tri-hexamer interface
ComponentsHIV-1 CA
KeywordsVIRAL PROTEIN / HIV-1 CA
Biological speciesHIV-1 group M (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsGoodale, A. / DiMaio, F. / Bergeron, J.R.C.
Funding support France, United Kingdom, 2items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGY0080/2021 France
Medical Research Council (MRC, United Kingdom)MR/W006820/1 United Kingdom
CitationJournal: bioRxiv / Year: 2026
Title: MX2 Mediates Collapse of the HIV-1 Capsid.
Authors: Andrew Goodale / Szu-Wei Huang / Nathalia Almeida / Dave J Williamson / Nikoloz Shkriabai / Gilberto Betancor / Luis Apolonia / Frank DiMaio / Sergi Padilla-Parra / Mamuka Kvaratskhelia / ...Authors: Andrew Goodale / Szu-Wei Huang / Nathalia Almeida / Dave J Williamson / Nikoloz Shkriabai / Gilberto Betancor / Luis Apolonia / Frank DiMaio / Sergi Padilla-Parra / Mamuka Kvaratskhelia / Julien R C Bergeron / Michael H Malim /
Abstract: The HIV-1 capsid core encapsulates the viral genome and mediates its delivery into the host cell's nucleus. It is composed of multiple copies of the Capsid (CA, p24) protein, assembled into hexamers ...The HIV-1 capsid core encapsulates the viral genome and mediates its delivery into the host cell's nucleus. It is composed of multiple copies of the Capsid (CA, p24) protein, assembled into hexamers and pentamers to create a lattice that forms a fullerene-like cone. Myxovirus resistance 2 (MX2) is an HIV-1 restriction factor that binds to the capsid core and blocks nuclear import of the viral genome. Here, we define a minimal region of MX2 required for HIV-1 restriction and produce a corresponding functional recombinant protein. We have used cryo-electron microscopy to determine the structure of this MX2 fragment bound to the tri-hexamer interface of the capsid lattice, revealing a large, buried interface combining electrostatic and hydrophobic interactions. This structure, together with assays that measure capsid core destabilisation, shows that MX2 binding induces conformational rearrangements in the capsid lattice that culminate in a loss of integrity. These results support a model whereby MX2 exerts its antiviral activity by disrupting the capsid lattice, inducing premature fragmentation and preventing HIV-1 nuclear import. By revealing the structural basis for MX2-mediated restriction, this work also provides the framework for the development of anti-HIV molecules that mimic MX2 restriction.
History
DepositionMay 5, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: HIV-1 CA
E: HIV-1 CA
e: HIV-1 CA
X: HIV-1 CA
Z: HIV-1 CA
a: HIV-1 CA


Theoretical massNumber of molelcules
Total (without water)154,5706
Polymers154,5706
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
HIV-1 CA


Mass: 25761.623 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 group M (virus) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HIV-1 CA tri-hexamer interface / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: HIV-1 group M (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 458221 / Symmetry type: POINT
RefinementHighest resolution: 4.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039395
ELECTRON MICROSCOPYf_angle_d0.53512735
ELECTRON MICROSCOPYf_dihedral_angle_d4.5161229
ELECTRON MICROSCOPYf_chiral_restr0.0391451
ELECTRON MICROSCOPYf_plane_restr0.0051628

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