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- EMDB-48674: HIV-1 capsid hepta-hexamer templated on small unilamellar vesicles. -

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Basic information

Entry
Database: EMDB / ID: EMD-48674
TitleHIV-1 capsid hepta-hexamer templated on small unilamellar vesicles.
Map dataHIV-1 hepta-hexamer from liposome templating on small unilamellar vesicles.
Sample
  • Complex: HIV-1 capsid protein p24 with C terminal hexahistidine tag
KeywordsCapsid / hexamer / HIV-1 / lattice / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsFreniere C / Arizaga F / Xiong Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170791 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI116313 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32GM008283 United States
CitationJournal: J Am Chem Soc / Year: 2025
Title: Exploring the Structural Divergence of HIV and SRLV Lentiviral Capsids.
Authors: Fidel Arizaga / Christian Freniere / Juan S Rey / Matthew Cook / Chunxiang Wu / Juan R Perilla / Yong Xiong /
Abstract: Lentiviruses require a mature capsid to package and traffic their viral genome for successful infection and propagation. Although the HIV-1 capsid structure has been extensively studied, structural ...Lentiviruses require a mature capsid to package and traffic their viral genome for successful infection and propagation. Although the HIV-1 capsid structure has been extensively studied, structural information is lacking for other lentiviral capsids, limiting our understanding. Using cryo-electron microscopy (cryo-EM) and a liposome-templating system, we assembled capsid-like particles (CLPs) and resolved capsid protein (CA) pentamer and hexamer lattice structures from the two major phylogenetic groups of small ruminant lentiviruses (SRLVs). These structures exhibit an overall lattice organization like HIV-1 but differ in key characteristics, notably the absence of inositol hexakisphosphate (IP6) in the SRLV CA lattice─a critical factor for HIV-1 capsid assembly and function. Additionally, SRLV CA pentamers show a unique N-terminal domain orientation, providing insights into SRLV capsid assembly mechanisms. These observations, together with our molecular dynamics (MD) simulation, results suggest a possible mechanism for importing deoxynucleotide triphosphate (dNTP) molecules into SRLV capsids. Furthermore, key regions of host factor interaction, such as the CypA binding motifs, have diverged in the SRLV CA assemblies. Our results contribute to understanding the SRLV lentiviral capsids which may facilitate structure-based inhibitor design strategies.
History
DepositionJan 16, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48674.png

Downloads & links

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Map

FileDownload / File: emd_48674.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 hepta-hexamer from liposome templating on small unilamellar vesicles.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 312.48 Å		0.87 Å/pix.
x 360 pix.
= 312.48 Å		0.87 Å/pix.
x 360 pix.
= 312.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.868 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.14473335 - 0.38016656
Average (Standard dev.)0.0015022111 (±0.0154574765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 312.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_48674_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_48674_half_map_2.map
Annotationhalf map B
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 capsid protein p24 with C terminal hexahistidine tag

EntireName: HIV-1 capsid protein p24 with C terminal hexahistidine tag
Components
  • Complex: HIV-1 capsid protein p24 with C terminal hexahistidine tag

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Supramolecule #1: HIV-1 capsid protein p24 with C terminal hexahistidine tag

SupramoleculeName: HIV-1 capsid protein p24 with C terminal hexahistidine tag
type: complex / ID: 1 / Parent: 0
Details: Protein was assembled onto small unilamellar vesicles with IP6 at pH 7.4
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 240 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration4.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES Buffer
125.0 mMKClPotassium Chloride
5.0 %C3H8O3Glycerol

Details: Hepes-buffered at pH 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Details: 11 mA 40s glow discharge in GloCube
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II / Details: Blot time 6.5 S Blot force 1.
DetailsHIV-1 capsid protein templated on small unilamellar vesicles with IP6

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Electron microscopy

MicroscopeTFS GLACIOS
TemperatureMin: 83.0 K / Max: 103.0 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Number real images: 3800 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 20.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 10000000
CTF correctionSoftware - Name: cryoSPARC / Details: Cryosparc's own implementation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

3465


Details: Lowpass filtered to 20 angstroms
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1428449
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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