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- PDB-9s28: MVV STC intasome in complex with LEDGF -

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Basic information

Entry
Database: PDB / ID: 9s28
TitleMVV STC intasome in complex with LEDGF
Components
  • DNA EV306
  • DNA EV391
  • DNA EV392
  • Gag-Pol polyprotein
  • PC4 and SFRS1-interacting protein
KeywordsVIRAL PROTEIN / integrase / LEDGF / p75 / MVV / DNA
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / supercoiled DNA binding / 2-LTR circle formation / Vpr-mediated nuclear import of PICs ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / supercoiled DNA binding / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Formation of WDR5-containing histone-modifying complexes / mRNA 5'-splice site recognition / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / heterochromatin / nuclear periphery / exoribonuclease H / exoribonuclease H activity / DNA integration / euchromatin / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral capsid / response to heat / response to oxidative stress / DNA recombination / DNA-directed DNA polymerase / DNA-binding transcription factor binding / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / transcription coactivator activity / chromatin remodeling / viral translational frameshifting / chromatin binding / symbiont entry into host cell / positive regulation of transcription by RNA polymerase II / proteolysis / DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / zinc ion binding / nucleus / cytosol
Similarity search - Function
Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / TFIIS/LEDGF domain superfamily / gag protein p24 N-terminal domain / domain with conserved PWWP motif ...Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / TFIIS/LEDGF domain superfamily / gag protein p24 N-terminal domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase-like, N-terminal / 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 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type 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
DNA / DNA (> 10) / PC4 and SFRS1-interacting protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesVisna/maedi virus EV1 KV1772
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPunch, E.K. / Hope, J. / Cherepanov, P.
Funding support United States, United Kingdom, 4items
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: Core nucleosomes are refractive for lentiviral integration
Authors: Hope, J. / Punch, E.K. / Cook, N.J. / Singer, M.R. / Joshi, D. / Singh, P.K. / Nans, A. / Engelman, A.N. / Cherepanov, P.
History
DepositionJul 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gag-Pol polyprotein
B: Gag-Pol polyprotein
C: Gag-Pol polyprotein
D: Gag-Pol polyprotein
E: Gag-Pol polyprotein
F: Gag-Pol polyprotein
G: Gag-Pol polyprotein
H: Gag-Pol polyprotein
I: Gag-Pol polyprotein
J: Gag-Pol polyprotein
K: Gag-Pol polyprotein
L: Gag-Pol polyprotein
M: Gag-Pol polyprotein
N: Gag-Pol polyprotein
O: Gag-Pol polyprotein
P: Gag-Pol polyprotein
a: PC4 and SFRS1-interacting protein
b: PC4 and SFRS1-interacting protein
c: PC4 and SFRS1-interacting protein
d: PC4 and SFRS1-interacting protein
e: PC4 and SFRS1-interacting protein
g: PC4 and SFRS1-interacting protein
h: PC4 and SFRS1-interacting protein
i: PC4 and SFRS1-interacting protein
j: PC4 and SFRS1-interacting protein
k: PC4 and SFRS1-interacting protein
T: DNA EV392
U: DNA EV392
W: DNA EV306
X: DNA EV391
Y: DNA EV306
Z: DNA EV391
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,198,65746
Polymers1,197,74132
Non-polymers91614
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

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Protein , 2 types, 26 molecules ABCDEFGHIJKLMNOPabcdeghijk

#1: Protein
Gag-Pol polyprotein


Mass: 32368.826 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Visna/maedi virus EV1 KV1772 / Strain: KV1772 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: P35956
#2: Protein
PC4 and SFRS1-interacting protein / CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived ...CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52


Mass: 60224.453 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: LEDGF/p75 protein / Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75475

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DNA chain , 3 types, 6 molecules TUWYXZ

#3: DNA chain DNA EV392


Mass: 9863.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA EV306


Mass: 8943.719 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA EV391


Mass: 19990.801 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)

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Non-polymers , 1 types, 14 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: Zn

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Details

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: MVV STC intasome in complex with LEDGF / Type: COMPLEX
Details: Integrase and LEDGF were produced in E. coli. The complex was assembled in vitro.
Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.902 MDa / Experimental value: NO
Source (natural)Organism: Visna-maedi virus / Strain: KV1772
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 150 mM NaCl, 20 mM BisTris-HCl pH 6.5, 3 mM CaCl2
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
EM embeddingMaterial: vitreous ice
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: 3300 nm / Nominal defocus min: 1500 nm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 7 eV

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
7UCSF Chimeramodel fitting
9PHENIX1.21.2_5419model refinement
10RELION4.0.0initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
12cryoSPARC4.5.3classification
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 60999
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60999 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17U32

7u32

17U321PDBexperimental model
23HPH

3hph

13HPH2PDBexperimental model
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00242888
ELECTRON MICROSCOPYf_angle_d0.40158484
ELECTRON MICROSCOPYf_dihedral_angle_d13.26516430
ELECTRON MICROSCOPYf_chiral_restr0.0386394
ELECTRON MICROSCOPYf_plane_restr0.0036998

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