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- EMDB-48430: SPA of purified HIV-1 CA protein in vitro assembled with IP6 (mat... -

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Basic information

Entry
Database: EMDB / ID: EMD-48430
TitleSPA of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 50 uM LEN was added post assembly.
Map dataRefine 3D map of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 50 uM LEN was added post assembly. Determined via SPA.
Sample
  • Virus: HIV-1 (virus)
    • Protein or peptide: Capsid protein p24
  • Ligand: Lenacapavir
  • Ligand: INOSITOL HEXAKISPHOSPHATE
KeywordsHIV / Mature / VLP / Lenacapavir / VIRUS LIKE PARTICLE
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
Biological speciesHomo sapiens (human) / HIV-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRicana CL / Dick RA
Funding support United States, 4 items
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 CL / Brancato SG / Highland CM / Ekbataniamiri F / Ambrus K / Rey JS / Faerch M / Perilla JR / Dick RA
History
DepositionDec 22, 2024-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48430.png

Downloads & links

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Map

FileDownload / File: emd_48430.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefine 3D map of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 50 uM LEN was added post assembly. Determined via SPA.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0018
Minimum - Maximum-0.003998664 - 0.008762086
Average (Standard dev.)0.000007525749 (±0.00041589414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48430_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Postprocess map of purified HIV-1 CA protein in...

Fileemd_48430_additional_1.map
AnnotationPostprocess map of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 50 uM LEN was added post assembly. Determined via SPA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refine 3D half2 map of purified HIV-1 CA...

Fileemd_48430_half_map_1.map
AnnotationRefine 3D half2 map of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 50 uM LEN was added post assembly. Determined via SPA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refine 3D half1 map of purified HIV-1 CA...

Fileemd_48430_half_map_2.map
AnnotationRefine 3D half1 map of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 50 uM LEN was added post assembly. Determined via SPA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1

EntireName: HIV-1 (virus)
Components
  • Virus: HIV-1 (virus)
    • Protein or peptide: Capsid protein p24
  • Ligand: Lenacapavir
  • Ligand: INOSITOL HEXAKISPHOSPHATE

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Supramolecule #1: HIV-1

SupramoleculeName: HIV-1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 50 uM LEN was added post assembly.
NCBI-ID: 11698 / Sci species name: HIV-1 / Sci species strain: NL4-3 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1000.0 Å

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Macromolecule #1: Capsid protein p24

MacromoleculeName: Capsid protein p24 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.630426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF ...String:
PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPG ATLEEMMTAC QGVGGPGHKA RVL

UniProtKB: Gag polyprotein

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Macromolecule #2: Lenacapavir

MacromoleculeName: Lenacapavir / type: ligand / ID: 2 / Number of copies: 3 / Formula: QNG
Molecular weightTheoretical: 968.282 Da

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Macromolecule #3: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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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

Concentration13 mg/mL
BufferpH: 6.2
Component:
ConcentrationFormulaName
25.0 mMC6H13NO4SMES
2.0 mMC9H15O6PTCEP
500.0 uMC39H32ClF10N7O5S2Lenacapavir

Details: 25 mM MES, 2mM TCEP, 500 uM LEN
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.027 kPa
Details: Vacuum held for 30 sec before 20 mA were applied for 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 279.15 K / Instrument: LEICA EM GP
DetailsPurified HIV-1 CASPNC protein in vitro assembled with IP6 (immature morphology). 50 uM LEN was added post assembly.

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 93.15 K / Max: 103.15 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 7510 / Average exposure time: 1.731 sec. / Average electron dose: 50.0 e/Å2
Details: Images were collected in movie-mode with 50 frames per image at a total dose of 50 e-/A2.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 25118581
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 594567
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Details: Iterative Bayesian sampling approach via RELION 5.0
Final 3D classificationSoftware - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8g6m


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsMolecular dynamics flexible fitting was done using NAMD targeting cross-correlation coefficients.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9mnm:
SPA of purified HIV-1 CA protein in vitro assembled with IP6 (mature morphology). 50 uM LEN was added post assembly.

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