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- EMDB-55409: HIV-1 integrase filament at the luminal side of capsid lattice by... -

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Basic information

Entry
Database: EMDB / ID: EMD-55409
TitleHIV-1 integrase filament at the luminal side of capsid lattice by subtomogram averaging.
Map dataLocally filtered map
Sample
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: HIV-1 capsid protein
    • Protein or peptide: HIV-1 integrase
KeywordsHIV-1 / retrovirus / capsid / RNA-binding protein / RNP / VIRUS
Function / homology
Function and homology information


exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / host cell / viral nucleocapsid / DNA recombination / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
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-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding 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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic 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. / 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
Methodsubtomogram averaging / cryo EM / Resolution: 12.56 Å
AuthorsCherepanov P / Chenavier F / Hope J / Nans A / Zhang P
Funding support United Kingdom, United States, 4 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)CC2058 United Kingdom
Wellcome TrustCC2058 United Kingdom
Cancer Research UKCC2058 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170791 United States
CitationJournal: To Be Published
Title: Structural bases for integrase-RNA binding and retention of viral RNA within HIV-1 capsid cores
Authors: Singer M / Li Z / Rey SJ / Hope J / Cook JN / Punch E / Smith J / Zhou Z / Maslen S / Masino L / Nans A / Skehel M / Taylor AI / Zhang P / Perilla JR / Engelman NA / Cherepanov P
History
DepositionOct 20, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55409.png

Downloads & links

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Map

FileDownload / File: emd_55409.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.02 Å/pix.
x 192 pix.
= 579.84 Å		3.02 Å/pix.
x 192 pix.
= 579.84 Å		3.02 Å/pix.
x 192 pix.
= 579.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.945
Minimum - Maximum-1.4292399 - 3.138341
Average (Standard dev.)0.039639868 (±0.39397702)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 579.83997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55409_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 1

Fileemd_55409_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_55409_half_map_2.map
Annotationhalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: HIV-1 capsid protein
    • Protein or peptide: HIV-1 integrase

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: HIV-1 capsid cores purified from lysed virions / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Sci species strain: NL4-3 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: HIV-1 capsid protein

MacromoleculeName: HIV-1 capsid protein / type: protein_or_peptide / ID: 1 / Details: HIV-1 capsid protein / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3
SequenceString: pivqnlqgqm vhqaisprtl nawvkvveek afspevipmf salsegatpq dlntmlntvg ghqaamqmlk etineeaaew drlhpvhagp iapgqmrepr gsdiagttst lqeqigwmth nppipvgeiy krwiilglnk ivrmysptsi ldirqgpkep frdyvdrfyk ...String:
pivqnlqgqm vhqaisprtl nawvkvveek afspevipmf salsegatpq dlntmlntvg ghqaamqmlk etineeaaew drlhpvhagp iapgqmrepr gsdiagttst lqeqigwmth nppipvgeiy krwiilglnk ivrmysptsi ldirqgpkep frdyvdrfyk tlraeqasqe vknwmtetll vqnanpdckt ilkalgpgat leemmtacqg vggpghkarv l

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Macromolecule #2: HIV-1 integrase

MacromoleculeName: HIV-1 integrase / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3
SequenceString: fldgidkaqe ehekyhsnwr amasdfnlpp vvakeivasc dkcqlkgeam hgqvdcspgi wqlncthleg kvilvavhva sgyieaevip aetgqetayf llklagrwpv ktvhtnngsn ftsttvkaac wwagikqefg ipynpqsqgv iesmnkelkk iigqvrdqae ...String:
fldgidkaqe ehekyhsnwr amasdfnlpp vvakeivasc dkcqlkgeam hgqvdcspgi wqlncthleg kvilvavhva sgyieaevip aetgqetayf llklagrwpv ktvhtnngsn ftsttvkaac wwagikqefg ipynpqsqgv iesmnkelkk iigqvrdqae hlktavqmav fihnfkrkgg iggysageri vdiiatdiqt kelqkqitki qnfrvyyrds rdpvwkgpak llwkgegavv iqdnsdikvv prrkakiird ygkqmagddc vasrqded

UniProtKB: Gag-Pol polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMTris-HCl
100.0 mMSodium chlorideNaCl
1.0 mMinositol hexaphosphate
Sugar embeddingMaterial: vitreous ice
GridModel: Quantifoil R2/2
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 1 / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 12.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 559
ExtractionNumber tomograms: 14 / Number images used: 2375 / Software: (Name: PyTom, RELION (ver. 4.0))
CTF correctionSoftware: (Name: RELION (ver. 4.0), Warp) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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