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- EMDB-80777: Cryo-EM Structure of the HIV Capsid in Complex with VHL-3 -

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Basic information

Entry
Database: EMDB / ID: EMD-80777
TitleCryo-EM Structure of the HIV Capsid in Complex with VHL-3
Map data
Sample
  • Complex: Cryo-EM Structure of the HIV Capsid in Complex with VHL-3
    • Protein or peptide: Capsid protein p24
  • Protein or peptide: 2LZ-WFP-A1E9U-BAL-TBG-HYP
  • Ligand: (1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethanamine
KeywordsHIV / Capsid / Inhibitor / VIRAL PROTEIN
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / 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 / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / 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 1 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsXue L / Gui J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32400116 China
CitationJournal: To Be Published
Title: Revolutionizing Anti-HIV Therapy: Targeted Degradation of Capsid by Host-Hijacking PROTAC Overcomes Drug Resistance
Authors: Xue L / Gui J
History
DepositionMay 7, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80777.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 240 pix.
= 210.24 Å		0.88 Å/pix.
x 240 pix.
= 210.24 Å		0.88 Å/pix.
x 240 pix.
= 210.24 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.876 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0016815051 - 1.7414722
Average (Standard dev.)0.0027834042 (±0.03981965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 210.23999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_80777_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80777_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_80777_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Cryo-EM Structure of the HIV Capsid in Complex with VHL-3

EntireName: Cryo-EM Structure of the HIV Capsid in Complex with VHL-3
Components
  • Complex: Cryo-EM Structure of the HIV Capsid in Complex with VHL-3
    • Protein or peptide: Capsid protein p24
  • Protein or peptide: 2LZ-WFP-A1E9U-BAL-TBG-HYP
  • Ligand: (1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethanamine

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Supramolecule #1: Cryo-EM Structure of the HIV Capsid in Complex with VHL-3

SupramoleculeName: Cryo-EM Structure of the HIV Capsid in Complex with VHL-3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Capsid protein p24

MacromoleculeName: Capsid protein p24 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 25.437229 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PIVQNIQGQM VHQCISPRTL NAWVKVVEEK AFSPEVIPMF SALSCGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRVHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT NNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF ...String:
PIVQNIQGQM VHQCISPRTL NAWVKVVEEK AFSPEVIPMF SALSCGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRVHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT NNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF YKTLRAEQAS QEVKNAATET LLVQNANPDC KTILKALGPA ATLEEMMTAC QGVGGPGHKA RVL

UniProtKB: Gag-Pol polyprotein

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Macromolecule #2: 2LZ-WFP-A1E9U-BAL-TBG-HYP

MacromoleculeName: 2LZ-WFP-A1E9U-BAL-TBG-HYP / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: DEXTRO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 841.272 Da
SequenceString:
(2LZ)(WFP)(A1E9U)(BAL)(TBG)(HYP)

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Macromolecule #3: (1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethanamine

MacromoleculeName: (1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethanamine
type: ligand / ID: 3 / Number of copies: 6 / Formula: A1E9V
Molecular weightTheoretical: 218.318 Da

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 3293231
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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