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- EMDB-54068: SIV Integrase in Complex With RNA Stem-Loop -

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Basic information

Entry
Database: EMDB / ID: EMD-54068
TitleSIV Integrase in Complex With RNA Stem-Loop
Map dataMap locally filtered using EMReady
Sample
  • Complex: Linear Polymer Assembly of SIV Integrase Octamers with RNA Stem-loop (local refinement).
    • Protein or peptide: Pol protein
    • RNA: RNA
  • Ligand: ZINC ION
KeywordsIntegrase / RNA / Octamer / SIVtal / VIRAL PROTEIN
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 / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / 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-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. / 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 speciesSimian immunodeficiency virus / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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 Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170791 United States
CitationJournal: To Be Published
Title: Structural basis for integrase-RNA binding and retention of viral RNA within HIV-1 capsid cores
Authors: Singer MR / Li Z / Rey JS / Hope J / Cook NJ / Punch 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 18, 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_54068.png

Downloads & links

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Map

FileDownload / File: emd_54068.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: 3.2
Minimum - Maximum-0.21548054 - 24.244700999999999
Average (Standard dev.)-0.0073589985 (±0.48377797)
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_54068_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 CroySPARC

Fileemd_54068_additional_1.map
AnnotationLocal filtered map by CroySPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_54068_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_54068_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-l...

EntireName: Linear Polymer Assembly of SIV Integrase Octamers with RNA Stem-loop (local refinement).
Components
  • Complex: Linear Polymer Assembly of SIV Integrase Octamers with RNA Stem-loop (local refinement).
    • Protein or peptide: Pol protein
    • RNA: RNA
  • Ligand: ZINC ION

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

SupramoleculeName: Linear Polymer Assembly of SIV Integrase Octamers with RNA Stem-loop (local refinement).
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Simian immunodeficiency virus

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Macromolecule #1: Pol protein

MacromoleculeName: Pol protein / type: protein_or_peptide / ID: 1
Details: This is the integrase protein of simian immunodeficiency virus (SIV) from the talapoin monkey (SIVtal).
Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Simian immunodeficiency virus
Molecular weightTheoretical: 33.424934 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: FVEQIPEAQE EHERYHNNWK DLKARFKLPT IVAKAIIEAC PKCQVQGEPK TGQTNAAVGT WQMDCTHLEG QVICVAVHVA SGYIETKIL PRETGRETAL FLLQVASRWP IEHLHTDNGP NFVSAEMQAT AWWLKIEHTT GVPYNPQSQG SVENKNKQLK K TIQQIRDE ...String:
FVEQIPEAQE EHERYHNNWK DLKARFKLPT IVAKAIIEAC PKCQVQGEPK TGQTNAAVGT WQMDCTHLEG QVICVAVHVA SGYIETKIL PRETGRETAL FLLQVASRWP IEHLHTDNGP NFVSAEMQAT AWWLKIEHTT GVPYNPQSQG SVENKNKQLK K TIQQIRDE VQYLSTAVAQ ATFILNFKRR GGLGDMCPAE ALINMIYTEL QTTTLQNQIH NFSDFKVYYR KGANPLWQGP AH LVWKGEG AVVLRTDEGE VITVPRRKAK IIKPYGQAMG NKTDLEGSKE QDAEMGRDN

UniProtKB: Pol protein

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2
Details: A 32-mer of RNA, in place to represent the double stranded section of HIV-1 TAR RNA.
Number of copies: 4
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.982484 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUAAAAAAAA AAAAAAAAAA AAAAAAA

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration0.134 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC8H18N2O4SHEPES

Details: 150 mM NaCl, 20 mM HEPES pH 8.0
Sugar embeddingMaterial: vitreous ice
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec.
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 model generated in cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 53737
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
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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