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- PDB-9mnm: SPA of purified HIV-1 CA protein in vitro assembled with IP6 (mat... -

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Basic information

Entry
Database: PDB / ID: 9mnm
TitleSPA of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly.
ComponentsHIV-1 CA
KeywordsVIRUS LIKE PARTICLE / HIV / Mature / VLP / Lenacapavir
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell plasma membrane / host cell nucleus / virion membrane / structural molecule activity / RNA binding / zinc ion binding
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / 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
INOSITOL HEXAKISPHOSPHATE / Chem-QNG / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 BH10
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRicana, C.L. / Dick, R.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI147890 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170855 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
National Science Foundation (NSF, United States)DMR-1719875 United States
CitationJournal: bioRxiv / Year: 2026
Title: Lenacapavir prevents production of infectious HIV-1 by abrogating immature virus assembly.
Authors: Clifton L Ricaña / Savannah G Brancato / Carolyn M Highland / Fatemeh Ekbataniamiri / Krisztina Ambrus / Juan S Rey / Mia Faerch / Bruce E Torbett / Juan R Perilla / Robert A Dick /
Abstract: The HIV-1 capsid effector Lenacapavir (LEN) acts by disrupting the early (reverse transcription and nuclear entry) and late (assembly and maturation) stages of the viral lifecycle. The early stage ...The HIV-1 capsid effector Lenacapavir (LEN) acts by disrupting the early (reverse transcription and nuclear entry) and late (assembly and maturation) stages of the viral lifecycle. The early stage requires an intact Capsid consisting of a lattice of capsid protein (CA) hexamers and pentamers. Phenylalanine-Glycine (FG) containing nuclear pore proteins interact with Capsid hexamers at their FG pockets, facilitating nuclear entry. Disruption of Capsid lattice stability, or competitive binding to the FG pocket, by LEN blocks infection. Here, we provide insight into the effects of LEN on the late stage. Using a combination of cryo-EM structure determination, assembly, and viral assays, we determined that treatment of producer cells with LEN abrogates the production of infectious virus via multiple mechanisms. Previous studies have shown that HIV-1 produced from LEN treated cells have improperly formed Capsids. However, how LEN interacts with the CA domain of the Gag polyprotein during assembly, prior to maturation, is unclear. Using a viral protease (PR) defective HIV-1 clone, which traps the Gag lattice in an immature state, we found that LEN dramatically remodulates the CA domain. The resulting CA layer was mature-like despite the absence of PR cleavage. We dubbed this unnatural state as "premature" lattice. Proper immature and mature lattice formation requires inositol hexakisphosphate (IP6), but our cryo-EM work revealed a lack of IP6 in the premature lattice. These findings provide insight into the mechanisms by which LEN prevents infectious HIV-1 production.
History
DepositionDec 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 CA
B: HIV-1 CA
C: HIV-1 CA
D: HIV-1 CA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7479
Polymers102,5224
Non-polymers4,2255
Water00
1
A: HIV-1 CA
B: HIV-1 CA
C: HIV-1 CA
D: HIV-1 CA
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)640,48054
Polymers615,13024
Non-polymers25,34930
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein
HIV-1 CA / Pr55Gag


Mass: 25630.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Strain: BH10 / Gene: Gag / Plasmid: pET SUMO / Details (production host): Thermo Champion / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: P12493
#2: Chemical ChemComp-QNG / Lenacapavir / Sunlenca / GS-CA1 / GS-6207


Mass: 968.282 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H32ClF10N7O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antiretroviral*YM
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: HIV-1 / Type: VIRUS
Details: Purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 500 uM LEN was added post assembly.
Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: HIV-1 (virus) / Strain: BH10
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: NiCo21(DE3) / Plasmid: pET SUMO
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellName: Capsid / Diameter: 1000 nm
Buffer solutionpH: 6.2 / Details: 25 mM MES, 2mM TCEP, 500 uM LEN
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMMESC6H13NO4S1
22 mMTCEPC9H15O6P1
3500 uMLenacapavirC39H32ClF10N7O5S21
SpecimenConc.: 13 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Purified HIV-1 CASPNC protein in vitro assembled with IP6 (immature morphology). 500 uM LEN was added post assembly.
Specimen supportDetails: Vacuum held for 30 sec before 20 mA were applied for 45 sec.
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: Preliminary grid screening was performed manually.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 103.15 K / Temperature (min): 93.15 K
Image recordingAverage exposure time: 1.731 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7510
Details: Images were collected in movie-mode with 50 frames per image at a total dose of 50 e-/A2.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 11520 / Height: 8184

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3.1particle selection
2SerialEM4.1image acquisition
4CTFFIND4.1.14CTF correction
7NAMD3.0.1model fitting
9cryoSPARC4.3.1initial Euler assignment
10RELION5final Euler assignment
11RELION5classification
12RELION53D reconstruction
13NAMD3.0.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 25118581
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 594567 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Molecular dynamics flexible fitting was done using NAMD targeting cross-correlation coefficients.
Atomic model buildingPDB-ID: 8G6M

8g6m


Accession code: 8G6M / Source name: PDB / Type: experimental model

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