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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). 50 uM LEN was added post assembly.
ComponentsCapsid protein p24
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 nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding ...viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
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 speciesHomo sapiens (human)
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: To Be Published
Title: Structural Analysis of HIV-1 Capsid Disruption by Lenacapavir Using Cryo-EM
Authors: Ricana, C.L. / Brancato, S.G. / Highland, C.M. / Ekbataniamiri, F. / Ambrus, K. / Rey, J.S. / Faerch, M. / Perilla, J.R. / Dick, R.A.
History
DepositionDec 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 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
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7479
Polymers102,5224
Non-polymers4,2255
Water00
1
A: Capsid protein p24
B: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
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
Capsid protein p24 / Pr55Gag


Mass: 25630.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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
#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). 50 uM LEN was added post assembly.
Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: HIV-1 (virus) / Strain: NL4-3
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). 50 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: 75 % / Chamber temperature: 279.15 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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