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- EMDB-54070: CryoEM reconstruction of integrase filament at the lumen of nativ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54070
TitleCryoEM reconstruction of integrase filament at the lumen of native HIV-1 cores (box size 47.3 nm)
Map dataMap locally filtered using EMReady
Sample
  • Virus: Human immunodeficiency virus 1
    • Protein or peptide: integrase
    • Protein or peptide: capsid
KeywordsHIV-1 / integrase octamer / capsid hexamer / RNA binding / VIRAL PROTEIN
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / viral nucleocapsid / endonuclease activity / DNA recombination ...DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / viral nucleocapsid / endonuclease activity / DNA recombination / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
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. / Integrase core domain / Integrase, catalytic core ...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. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.85 Å
AuthorsCherepanov P / Singer MR / Hope J / Zhang P
Funding support United States, United Kingdom, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170791 United States
Wellcome TrustCC2058 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2058 United Kingdom
Cancer Research UKCC2058 United Kingdom
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 JS / Hope J / Cook NJ / Puch E / Smith J / Zhou Z / Maslen S / Masino L / Nans A / Skehel M / Taylor IA / Zhang P / Perilla JR / Engelman AN / Cherepanov P
History
DepositionJun 19, 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_54070.png

Downloads & links

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Map

FileDownload / File: emd_54070.map.gz / Format: CCP4 / Size: 139.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap locally filtered using EMReady
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 332 pix.
= 473.1 Å		1.43 Å/pix.
x 332 pix.
= 473.1 Å		1.43 Å/pix.
x 332 pix.
= 473.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.425 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.59
Minimum - Maximum-0.10594257 - 12.561370999999999
Average (Standard dev.)0.10718712 (±0.6819789)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions332332332
Spacing332332332
CellA=B=C: 473.09998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54070_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Globally sharpened map from CryoSPARC

Fileemd_54070_additional_1.map
AnnotationGlobally sharpened map from CryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 1

Fileemd_54070_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_54070_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: integrase
    • Protein or peptide: capsid

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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: virus was produced by transfection of HEK293T cells with molecular clone
NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Sci species strain: NL4-3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / Strain: NL4-3

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Macromolecule #1: integrase

MacromoleculeName: integrase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3
Recombinant expressionOrganism: Homo sapiens (human)
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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Macromolecule #2: capsid

MacromoleculeName: capsid / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3
Recombinant expressionOrganism: Homo sapiens (human)
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

UniProtKB: Gag-Pol polyprotein

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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: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
25.0 mMTris-HClTris hydrochloride
1.0 mMIP6inositol hexaphosphate
Sugar embeddingMaterial: vitreous ice
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 49.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 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: OTHER / Details: Ab initio reconstruction in CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 46116
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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