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- EMDB-45760: HIV-2 CA hexamer bound with Nup153 peptide; assembled with liposo... -

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Entry
Database: EMDB / ID: EMD-45760
TitleHIV-2 CA hexamer bound with Nup153 peptide; assembled with liposome templating
Map dataEM map of HIV-2 CA hexamers assembled via liposome templating with Nup153 peptide allowed to bind.
Sample
  • Complex: HIV-2 capsid protein assembled into a lattice via liposome templating and then bound with Nup153 peptide.
    • Complex: HIV-2 capsid protein
      • Protein or peptide: Capsid protein p24
    • Complex: Nup153 peptide
      • Protein or peptide: Nuclear pore complex protein Nup153
  • Ligand: INOSITOL HEXAKISPHOSPHATE
KeywordsHIV-2 / Capsid / IP6 / Nup153 / VIRAL PROTEIN
Function / homology
Function and homology information


HIV-2 retropepsin / negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / Transport of Ribonucleoproteins into the Host Nucleus / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA ...HIV-2 retropepsin / negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / Transport of Ribonucleoproteins into the Host Nucleus / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / nuclear localization sequence binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / RNA export from nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / SUMOylation of DNA damage response and repair proteins / protein-membrane adaptor activity / nuclear periphery / SUMOylation of chromatin organization proteins / HCMV Late Events / Transcriptional regulation by small RNAs / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / molecular condensate scaffold activity / host multivesicular body / DNA integration / ISG15 antiviral mechanism / 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 / HCMV Early Events / protein import into nucleus / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nuclear envelope / host cell / snRNP Assembly / viral nucleocapsid / DNA recombination / nuclear membrane / amyloid fibril formation / 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 / nucleolus / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / membrane / cytosol
Similarity search - Function
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. ...Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / 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
Gag-Pol polyprotein / Nuclear pore complex protein Nup153
Similarity search - Component
Biological speciesHuman immunodeficiency virus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 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_45760.png

Downloads & links

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Map

FileDownload / File: emd_45760.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of HIV-2 CA hexamers assembled via liposome templating with Nup153 peptide allowed to bind.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 180 pix.
= 192.24 Å		1.07 Å/pix.
x 180 pix.
= 192.24 Å		1.07 Å/pix.
x 180 pix.
= 192.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.17847843 - 0.51358736
Average (Standard dev.)0.0142483795 (±0.036727317)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 192.23999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half map A of HIV-2 CA hexamer bound with Nup153 peptide.

Fileemd_45760_half_map_1.map
AnnotationEM half map A of HIV-2 CA hexamer bound with Nup153 peptide.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map B of HIV-2 CA hexamer bound with Nup153 peptide.

Fileemd_45760_half_map_2.map
AnnotationEM half map B of HIV-2 CA hexamer bound with Nup153 peptide.
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 templa...

EntireName: HIV-2 capsid protein assembled into a lattice via liposome templating and then bound with Nup153 peptide.
Components
  • Complex: HIV-2 capsid protein assembled into a lattice via liposome templating and then bound with Nup153 peptide.
    • Complex: HIV-2 capsid protein
      • Protein or peptide: Capsid protein p24
    • Complex: Nup153 peptide
      • Protein or peptide: Nuclear pore complex protein Nup153
  • Ligand: INOSITOL HEXAKISPHOSPHATE

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

SupramoleculeName: HIV-2 capsid protein assembled into a lattice via liposome templating and then bound with Nup153 peptide.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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. Nup153 peptide is subsequently ...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. Nup153 peptide is subsequently introduced and binding is allowed to equilibrate.
Molecular weightTheoretical: 26.9 KDa

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Supramolecule #2: HIV-2 capsid protein

SupramoleculeName: HIV-2 capsid protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 2 / Strain: GL-AN

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Supramolecule #3: Nup153 peptide

SupramoleculeName: Nup153 peptide / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes

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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 followed by a hexahistidine tag after proteolytic processing of the N-terminal Met.
Number of copies: 1 / 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: Nuclear pore complex protein Nup153

MacromoleculeName: Nuclear pore complex protein Nup153 / type: protein_or_peptide / ID: 2
Details: Peptide of Nup153, residues 1411-1425 and 1464-1475
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.897363 KDa
SequenceString:
PSGVFTFGAN SSTPAGRKIK TAVRRRK

UniProtKB: Nuclear pore complex protein Nup153, Nuclear pore complex protein Nup153

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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

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 / Support film - Film thickness: 12 / 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 final concentrations after subsequent addition. Nup153 peptide was then introduced to 400 uM final concentration. 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: 11931864
Startup modelType of model: EMDB MAP
EMDB ID:

3465

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1494376
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. The peptide was modeled by backbone tracing.
RefinementSpace: REAL / Protocol: OTHER / Target criteria: Cross-correlation coefficient
Output model

PDB-9cnu:
HIV-2 CA hexamer bound with Nup153 peptide; assembled with liposome templating

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