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- EMDB-45758: HIV-2 CA hexamer; assembled via liposome templating -

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Basic information

Entry
Database: EMDB / ID: EMD-45758
TitleHIV-2 CA hexamer; assembled via liposome templating
Map dataEM map of the HIV-2 CA hexamer surrounded by CA hexamers assembled via templating on functionalized liposomes.
Sample
  • Complex: HIV-2 capsid protein assembled into a lattice via liposome templating.
    • Protein or peptide: Capsid protein p24
  • Ligand: INOSITOL HEXAKISPHOSPHATE
KeywordsHIV-2 / Capsid / IP6 / VIRAL PROTEIN
Function / homology
Function and homology information


HIV-2 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity ...HIV-2 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral ...gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 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
DepositionJul 15, 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_45758.png

Downloads & links

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Map

FileDownload / File: emd_45758.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of the HIV-2 CA hexamer surrounded by CA hexamers assembled via templating on functionalized liposomes.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 416 pix.
= 451.776 Å		1.09 Å/pix.
x 416 pix.
= 451.776 Å		1.09 Å/pix.
x 416 pix.
= 451.776 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.086 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.17752485 - 0.5912113
Average (Standard dev.)0.0051829414 (±0.02701715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 451.776 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half map B of the HIV-2 CA hexamer surrounded by CA hexamers.

Fileemd_45758_half_map_1.map
AnnotationEM half map B of the HIV-2 CA hexamer surrounded by CA hexamers.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map A of the HIV-2 CA hexamer surrounded by CA hexamers.

Fileemd_45758_half_map_2.map
AnnotationEM half map A of the HIV-2 CA hexamer surrounded by CA hexamers.
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-2 capsid protein assembled into a lattice via liposome templating.

EntireName: HIV-2 capsid protein assembled into a lattice via liposome templating.
Components
  • Complex: HIV-2 capsid protein assembled into a lattice via liposome templating.
    • Protein or peptide: Capsid protein p24
  • Ligand: INOSITOL HEXAKISPHOSPHATE

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Supramolecule #1: HIV-2 capsid protein assembled into a lattice via liposome templating.

SupramoleculeName: HIV-2 capsid protein assembled into a lattice via liposome templating.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: C-terminally hexahistidine tagged HIV-2 CA associated with a liposome decorated with NiNTA headgroups which results in the assembly of a lattice of CA.
Source (natural)Organism: Human immunodeficiency virus 2 / Strain: GL-AN
Molecular weightTheoretical: 26.9 KDa

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Macromolecule #1: Capsid protein p24

MacromoleculeName: Capsid protein p24 / type: protein_or_peptide / ID: 1
Details: HIV-2 GL-AN capsid protein with C-terminal Gly-Ser-Ser linker to hexahistidine tag following proteolytic cleavage of the N-terminal Met.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 2 / Strain: GL-AN
Molecular weightTheoretical: 26.80949 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PVQQTGGGNY IHVPLSPRTL NAWVKLVEDK KFGAEVVPGF QALSEGCTPY DINQMLNCVG DHQAAMQIIR EIINDEAADW DAQHPIPGP LPAGQLRDPR GSDIAGTTST VEEQIQWMYR PQNPVPVGNI YRRWIQIGLQ KCVRMYNPTN ILDVKQGPKE P FQSYVDRF ...String:
PVQQTGGGNY IHVPLSPRTL NAWVKLVEDK KFGAEVVPGF QALSEGCTPY DINQMLNCVG DHQAAMQIIR EIINDEAADW DAQHPIPGP LPAGQLRDPR GSDIAGTTST VEEQIQWMYR PQNPVPVGNI YRRWIQIGLQ KCVRMYNPTN ILDVKQGPKE P FQSYVDRF YKSLRAEQTD PAVKNWMTQT LLIQNANPDC KLVLKGLGMN PTLEEMLTAC QGVGGPGQKA RLMGSSHHHH HH

UniProtKB: Gag-Pol polyprotein

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Macromolecule #2: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 2 / 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

Concentration10.7 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
20.0 mMHEPES
250.0 mMSodium chlorideNaCl
0.1 mMTCEP
4.0 mMIP6

Details: The mixed buffer of storage buffer for the protein and lipid components with IP6 supplemented.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.015 kPa / Details: 15 mA discharge current.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Details: Grids were dual-side blotted with blot force 0 for 5.5 sec before plunge freezing in liquid ethane..
DetailsSample was prepared with 400 uM HIV-2 CA-6xHis protein, 5.9 mM lipid mix (described in publication), and 4 mM IP6. Sample was well-distributed on the grid, mostly monodisperse. Perhaps slightly more particles on carbon versus in the hole.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 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: 0.8 µm / Nominal magnification: 81000
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: 13209858
Startup modelType of model: EMDB MAP
EMDB ID:

3465

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 603473
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9clj


Chain - Chain ID: A / Chain - Residue range: 1-223 / Chain - Source name: Other / Chain - Initial model type: experimental model
Details: NTDs matched well, but the CTD had to be realigned.
DetailsThe HIV-2 CA pentamer chain derived from micelle-templated icosahedra described in this publication was used as an initial model for fitting. Flexible fitting was used to move the CTD into its proper location.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9cns:
HIV-2 CA hexamer; assembled via liposome templating

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