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- PDB-9rmu: SIVtal integrase in complex with RNA stem-loop (focused refinemen... -

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Basic information

Entry
Database: PDB / ID: 9rmu
TitleSIVtal integrase in complex with RNA stem-loop (focused refinement of the filament repeat unit)
Components
  • Pol protein
  • RNA
KeywordsVIRAL PROTEIN / Integrase / RNA / Octamer / SIVtal
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
RNA / RNA (> 10) / Pol protein
Similarity search - Component
Biological speciesSimian immunodeficiency virus
Human immunodeficiency virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSinger, M.R. / Cherepanov, P.
Funding support United Kingdom, United States, 5items
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, M.R. / Li, Z. / Rey, J.S. / Hope, J. / Cook, N.J. / Punch, E. / Smith, J. / Zhou, Z. / Maslen, S. / Masino, L. / Nans, A. / Skehel, M. / Taylor, I.A. / Zhang, P. / Perilla, J.R. / ...Authors: Singer, M.R. / Li, Z. / Rey, J.S. / Hope, J. / Cook, N.J. / Punch, E. / Smith, J. / Zhou, Z. / Maslen, S. / Masino, L. / Nans, A. / Skehel, M. / Taylor, I.A. / Zhang, P. / Perilla, J.R. / Engelman, A.N. / Cherepanov, P.
History
DepositionJun 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2025Group: Data collection / Structure summary / Category: em_admin / struct
Item: _em_admin.last_update / _em_admin.title / _struct.title
Revision 1.1Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_admin.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pol protein
B: Pol protein
C: Pol protein
D: Pol protein
J: RNA
b: Pol protein
E: Pol protein
F: Pol protein
G: Pol protein
H: Pol protein
I: RNA
f: Pol protein
j: RNA
i: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,83324
Polymers406,17914
Non-polymers65410
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Pol protein


Mass: 33424.934 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: This is the integrase protein of simian immunodeficiency virus (SIV) from the talapoin monkey (SIVtal).
Source: (gene. exp.) Simian immunodeficiency virus / Gene: POL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): PC2 / References: UniProt: Q1XE75
#2: RNA chain
RNA


Mass: 17982.484 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: A 32-mer of RNA, in place to represent the double stranded section of HIV-1 TAR RNA.
Source: (synth.) Human immunodeficiency virus 1
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Linear Polymer Assembly of SIV Integrase Octamers with RNA Stem-loop (local refinement).
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Simian immunodeficiency virus
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Details of virusIsolate: SUBSPECIES / Type: VIRION
Buffer solutionpH: 8 / Details: 150 mM NaCl, 20 mM HEPES pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMHEPESC8H18N2O4S1
SpecimenConc.: 0.134 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: After glow discharging for 5 minutes at 25 mA, the grids were coated with graphene oxide.
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
EM embeddingMaterial: vitreous ice
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 41 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2Topazparticle selection
3Gautomatchparticle selection
4EPUimage acquisition
9UCSF Chimeramodel fitting
11cryoSPARC4.5.3initial Euler assignment
12cryoSPARC4.5.3final Euler assignment
13cryoSPARC4.5.3classification
14cryoSPARC4.5.33D reconstruction
15PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53737 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00219422
ELECTRON MICROSCOPYf_angle_d0.43126632
ELECTRON MICROSCOPYf_dihedral_angle_d5.1023095
ELECTRON MICROSCOPYf_chiral_restr0.0373014
ELECTRON MICROSCOPYf_plane_restr0.0033188

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