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- EMDB-47600: HIV-1 Global CA Pentamer Assembled by Liposome Templating on Smal... -

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Basic information

Entry
Database: EMDB / ID: EMD-47600
TitleHIV-1 Global CA Pentamer Assembled by Liposome Templating on Small Unilamellar Vesicles
Map dataHIV-1 capsid lattice assembled via liposome templating using small unilamellar vesicles.
Sample
  • Complex: HIV-1 capsid protein lattice assembled via liposome templating using small unilamellar vesicles.
    • Protein or peptide: HIV-1 capsid protein with C-terminal hexahistidine tag
KeywordsCapsid / HIV-1 / Liposome / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsFreniere C / Cook M / Xiong Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32GM008283 United States
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)P50AI150481 United States
CitationJournal: Cell Rep / Year: 2025
Title: Structural insights into HIV-2 CA lattice formation and FG-pocket binding revealed by single-particle cryo-EM.
Authors: Matthew Cook / Christian Freniere / Chunxiang Wu / Faith Lozano / Yong Xiong /
Abstract: One of the striking features of human immunodeficiency virus (HIV) is the capsid, a fullerene cone comprised of pleomorphic capsid protein (CA) that shields the viral genome and recruits cofactors. ...One of the striking features of human immunodeficiency virus (HIV) is the capsid, a fullerene cone comprised of pleomorphic capsid protein (CA) that shields the viral genome and recruits cofactors. Despite significant advances in understanding the mechanisms of HIV-1 CA assembly and host factor interactions, HIV-2 CA assembly remains poorly understood. By templating the assembly of HIV-2 CA on functionalized liposomes, we report high-resolution structures of the HIV-2 CA lattice, including both CA hexamers and pentamers, alone and with peptides of host phenylalanine-glycine (FG)-motif proteins Nup153 and CPSF6. While the overall fold and mode of FG-peptide binding is conserved with HIV-1, this study reveals distinctive features of the HIV-2 CA lattice, including differing structural character at regions of host factor interactions and divergence in the mechanism of formation of CA hexamers and pentamers. This study extends our understanding of HIV capsids and highlights an approach facilitating the study of lentiviral capsid biology.
History
DepositionOct 31, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47600.png

Downloads & links

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Map

FileDownload / File: emd_47600.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 capsid lattice assembled via liposome templating using 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: 0.08
Minimum - Maximum-0.10238432 - 0.33505702
Average (Standard dev.)0.003299351 (±0.018111743)
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 B of HIV-1 capsid lattice assembled via liposome templating.

Fileemd_47600_half_map_1.map
AnnotationHalf map B of HIV-1 capsid lattice assembled via liposome templating.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of HIV-1 capsid lattice assembled via liposome templating.

Fileemd_47600_half_map_2.map
AnnotationHalf map A of HIV-1 capsid lattice assembled via liposome templating.
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 lattice assembled via liposome templating us...

EntireName: HIV-1 capsid protein lattice assembled via liposome templating using small unilamellar vesicles.
Components
  • Complex: HIV-1 capsid protein lattice assembled via liposome templating using small unilamellar vesicles.
    • Protein or peptide: HIV-1 capsid protein with C-terminal hexahistidine tag

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Supramolecule #1: HIV-1 capsid protein lattice assembled via liposome templating us...

SupramoleculeName: HIV-1 capsid protein lattice assembled via liposome templating using small unilamellar vesicles.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: HIV-1 capsid protein with hexahistidine tag was recombinantly expressed and purified to homogeneity. The protein was then induced to assemble by templating on liposomes.
Source (natural)Organism: Human immunodeficiency virus 1

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

MacromoleculeName: HIV-1 capsid protein with C-terminal hexahistidine tag
type: protein_or_peptide / ID: 1
Details: Contains a C-terminal hexahistidine tag with intervening Gly-Ser-Ser linker.
Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PIVQNLQGQM VHQCISPRTL NAWVKVVEEK AFSPEVIPMF SALSCGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAGP IAPGQMREPR GSDIAGTTST LQEQIGWMTH NPPIPVGEIY KRWIILGLNK IVRMYSPTSI LDIRQGPKEP FRDYVDRFYK ...String:
PIVQNLQGQM VHQCISPRTL NAWVKVVEEK AFSPEVIPMF SALSCGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAGP IAPGQMREPR GSDIAGTTST LQEQIGWMTH NPPIPVGEIY KRWIILGLNK IVRMYSPTSI LDIRQGPKEP FRDYVDRFYK TLRAEQASQE VKNAATETLL VQNANPDCKT ILKALGPGAT LEEMMTACQG VGGPGHKARV LGSSHHHHHH

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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

Concentration5.0 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.015 kPa / Details: Discharge current was 15 mA.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time: 6.5 sec. Blot force: 1.
DetailsSample is evenly dispersed.

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Electron microscopy

MicroscopeTFS GLACIOS
TemperatureMin: 88.0 K / Max: 103.0 K
DetailsGrid was manually screened.
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3611 / 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: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 73000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

DetailsMotion corrected using CryoSPARC's own implementation.
Particle selectionNumber selected: 7600275
Details: Templates were generated from manual picking and 2D classification.
Startup modelType of model: EMDB MAP
EMDB ID:

3465


Details: Low-pass filtered to 40 A for template in heterogeneous refinement.
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 745724
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Ab initio reconstruction.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Local refinement.
FSC plot (resolution estimation)

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