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- EMDB-54067: SIVtal integrase in complex with RNA stem-loop (double filament r... -

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Basic information

Entry
Database: EMDB / ID: EMD-54067
TitleSIVtal integrase in complex with RNA stem-loop (double filament reconstructed by global refinement)
Map dataMap locally filtered using EMReady.
Sample
  • Complex: Linear Polymer Assembly of SIV Integrase Octamers with RNA Stem-loop.
KeywordsIntegrase / polymer / RNA / SIV / VIRAL PROTEIN
Biological speciesSimian immunodeficiency virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsSinger MR / Cherepanov P
Funding support United Kingdom, United States, 5 items
OrganizationGrant numberCountry
Cancer Research UKCC2058 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2058 United Kingdom
Wellcome TrustCC2058 United Kingdom
The Francis Crick InstituteCC2058 United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)U54AI170791 United States
CitationJournal: To Be Published
Title: Structure of Linear Polymer Assembly of SIV Integrase-TAR RNA Complexes
Authors: Singer MR / Cherepanov P
History
DepositionJun 18, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54067.png

Downloads & links

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Map

FileDownload / File: emd_54067.map.gz / Format: CCP4 / Size: 244.1 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.)
0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.83
Minimum - Maximum-0.20881544 - 22.990593000000001
Average (Standard dev.)0.036743596 (±0.62032026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 380.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54067_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local filtered map by CryoSPARC

Fileemd_54067_additional_1.map
AnnotationLocal filtered map by CryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_54067_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_54067_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Linear Polymer Assembly of SIV Integrase Octamers with RNA Stem-loop.

EntireName: Linear Polymer Assembly of SIV Integrase Octamers with RNA Stem-loop.
Components
  • Complex: Linear Polymer Assembly of SIV Integrase Octamers with RNA Stem-loop.

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Supramolecule #1: Linear Polymer Assembly of SIV Integrase Octamers with RNA Stem-loop.

SupramoleculeName: Linear Polymer Assembly of SIV Integrase Octamers with RNA Stem-loop.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Simian immunodeficiency virus

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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
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC8H18N2O4SHEPES

Details: 150 mM NaCl, 20 mM HEPES pH 8.0
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Pretreatment - Atmosphere: OTHER
Details: After glow discharging for 5 minutes at 25 mA, the grids were coated with graphene oxide.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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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: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 53737
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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