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- EMDB-13077: Structure of the STLV intasome:B56 complex bound to the strand-tr... -

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Basic information

Entry
Database: EMDB / ID: EMD-13077
TitleStructure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor bictegravir
Map dataDeepEMenhancer highest target map
Sample
  • Complex: Complex of STLV-1 MarB43 integrase with nascent viral DNA, the human PP2A B56 subunit and the drug inhibitor bictegravir
    • Complex: Integrase
      • Protein or peptide: Integrase
    • Complex: PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
      • Protein or peptide: PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
    • Complex: DNA
      • DNA: DNA (5'-D(*AP*CP*TP*GP*TP*GP*TP*TP*TP*GP*GP*CP*GP*CP*TP*TP*CP*TP*CP*TP*C)-3')
      • DNA: DNA (5'-D(*GP*AP*GP*AP*GP*AP*AP*GP*CP*GP*CP*CP*AP*AP*AP*CP*AP*CP*A)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: Bictegravir
  • Ligand: water
Keywordsintegrase / intasome / HTLV / STLV / integration / strand-transfer inhibitors / INSTI / bictegravir / BIC / drug / VIRAL PROTEIN
Function / homology
Function and homology information


DNA integration / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / zinc ion binding
Similarity search - Function
Integrase Zinc binding domain / Integrase DNA binding domain / 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. / Ribonuclease H domain ...Integrase Zinc binding domain / Integrase DNA binding domain / 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. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesSimian T-lymphotropic virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBarski MS / Ballandras-Colas A
Funding support United Kingdom, United States, 4 items
OrganizationGrant numberCountry
Wellcome Trust107005/Z/15Z United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)GM082251 United States
The Francis Crick InstituteFC001061 United Kingdom
Wellcome Trust206175/Z/17/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures.
Authors: Michal S Barski / Teresa Vanzo / Xue Zhi Zhao / Steven J Smith / Allison Ballandras-Colas / Nora B Cronin / Valerie E Pye / Stephen H Hughes / Terrence R Burke / Peter Cherepanov / Goedele N Maertens /
Abstract: Between 10 and 20 million people worldwide are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). Despite causing life-threatening pathologies there is no therapeutic regimen for this ...Between 10 and 20 million people worldwide are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). Despite causing life-threatening pathologies there is no therapeutic regimen for this deltaretrovirus. Here, we screened a library of integrase strand transfer inhibitor (INSTI) candidates built around several chemical scaffolds to determine their effectiveness in limiting HTLV-1 infection. Naphthyridines with substituents in position 6 emerged as the most potent compounds against HTLV-1, with XZ450 having highest efficacy in vitro. Using single-particle cryo-electron microscopy we visualised XZ450 as well as the clinical HIV-1 INSTIs raltegravir and bictegravir bound to the active site of the deltaretroviral intasome. The structures reveal subtle differences in the coordination environment of the Mg ion pair involved in the interaction with the INSTIs. Our results elucidate the binding of INSTIs to the HTLV-1 intasome and support their use for pre-exposure prophylaxis and possibly future treatment of HTLV-1 infection.
History
DepositionJun 11, 2021-
Header (metadata) releaseAug 18, 2021-
Map releaseAug 18, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ouh
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13077.png

Downloads & links

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Map

FileDownload / File: emd_13077.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMenhancer highest target map
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.0656 / Movie #1: 0.1
Minimum - Maximum-0.026005248 - 1.9995933
Average (Standard dev.)0.0010947615 (±0.023843197)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 334.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z304304304
origin x/y/z0.0000.0000.000
length x/y/z334.400334.400334.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ540540540
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-0.0262.0000.001

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Supplemental data

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Additional map: denmod map - model was refined against this map

Fileemd_13077_additional_1.map
Annotationdenmod map - model was refined against this map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_13077_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_13077_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 : Complex of STLV-1 MarB43 integrase with nascent viral DNA, the hu...

EntireName: Complex of STLV-1 MarB43 integrase with nascent viral DNA, the human PP2A B56 subunit and the drug inhibitor bictegravir
Components
  • Complex: Complex of STLV-1 MarB43 integrase with nascent viral DNA, the human PP2A B56 subunit and the drug inhibitor bictegravir
    • Complex: Integrase
      • Protein or peptide: Integrase
    • Complex: PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
      • Protein or peptide: PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
    • Complex: DNA
      • DNA: DNA (5'-D(*AP*CP*TP*GP*TP*GP*TP*TP*TP*GP*GP*CP*GP*CP*TP*TP*CP*TP*CP*TP*C)-3')
      • DNA: DNA (5'-D(*GP*AP*GP*AP*GP*AP*AP*GP*CP*GP*CP*CP*AP*AP*AP*CP*AP*CP*A)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: Bictegravir
  • Ligand: water

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Supramolecule #1: Complex of STLV-1 MarB43 integrase with nascent viral DNA, the hu...

SupramoleculeName: Complex of STLV-1 MarB43 integrase with nascent viral DNA, the human PP2A B56 subunit and the drug inhibitor bictegravir
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Sample composition and source have been described in "macromolecules"
Molecular weightTheoretical: 331.1 KDa

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Supramolecule #2: Integrase

SupramoleculeName: Integrase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Simian T-lymphotropic virus 1

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Supramolecule #3: PC4 and SFRS1-interacting protein,Serine/threonine-protein phosph...

SupramoleculeName: PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Simian T-lymphotropic virus 1

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Macromolecule #1: Integrase

MacromoleculeName: Integrase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Simian T-lymphotropic virus 1
Molecular weightTheoretical: 33.943539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPEFQLSPAK LHSFTHCGQA ALTLHGATTT EALNILHSCH ACRKNNPQHQ MPRGHIRRGL LPNHIWQGDI THFKYKNTLY RLHVWVDTF SGSVSATHKK RETSSEAISS LLHAIAHLGR PSHINTDNGP AYASQEFQHA CTSLAIRHTT HIPYNPTSSG L VERTNGIL ...String:
GPEFQLSPAK LHSFTHCGQA ALTLHGATTT EALNILHSCH ACRKNNPQHQ MPRGHIRRGL LPNHIWQGDI THFKYKNTLY RLHVWVDTF SGSVSATHKK RETSSEAISS LLHAIAHLGR PSHINTDNGP AYASQEFQHA CTSLAIRHTT HIPYNPTSSG L VERTNGIL KTLLYKYFSD NPNLPMDNAL SVALWTINHL NVLTHCQKTR WQLHHSPRLP PIPEEKPVTT SKTHWYYFKI PG LNSRQWK GPQRALQEAA GAALIPVSDT AAQWIPWKLL KRAVCPRLAG DTADPKERDH QHHG

UniProtKB: Pol protein

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Macromolecule #2: PC4 and SFRS1-interacting protein,Serine/threonine-protein phosph...

MacromoleculeName: PC4 and SFRS1-interacting protein,Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
type: protein_or_peptide / ID: 2
Details: fusion construct containing human LEDGF (residues 1-324 thus without the IBD domain) (gene PSIP1; O75475)) and human B56gammma (residues 11-380) regulatory subunit of PP2A (gene PPP2R5C) (no ...Details: fusion construct containing human LEDGF (residues 1-324 thus without the IBD domain) (gene PSIP1; O75475)) and human B56gammma (residues 11-380) regulatory subunit of PP2A (gene PPP2R5C) (no space for these details below),fusion construct containing human LEDGF (residues 1-324 thus without the IBD domain) (gene PSIP1; O75475)) and human B56gammma (residues 11-380) regulatory subunit of PP2A (gene PPP2R5C) (no space for these details below)
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.39468 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMTRDFKPGD LIFAKMKGYP HWPARVDEVP DGAVKPPTNK LPIFFFGTHE TAFLGPKDIF PYSENKEKYG KPNKRKGFNE GLWEIDNNP KVKFSSQQAA TKQSNASSDV EVEEKETSVS KEDTDHEEKA SNEDVTKAVD ITTPKAARRG RKRKAEKQVE T EEAGVVTT ...String:
SMTRDFKPGD LIFAKMKGYP HWPARVDEVP DGAVKPPTNK LPIFFFGTHE TAFLGPKDIF PYSENKEKYG KPNKRKGFNE GLWEIDNNP KVKFSSQQAA TKQSNASSDV EVEEKETSVS KEDTDHEEKA SNEDVTKAVD ITTPKAARRG RKRKAEKQVE T EEAGVVTT ATASVNLKVS PKRGRPAATE VKIPKPRGRP KMVKQPCPSE SDIITEEDKS KKKGQEEKQP KKQPKKDEEG QK EEDKPRK EPDKKEGKKE VESKRKNLAK TGVTSTSDSE EEGDDQEGEK KRKGGRNFQT AHRRNMLKGQ HEKEAADRKR KQE EQMETE FMVVDAANSN GPFQPVVLLH IRDVPPADQE KLFIQKLRQC CVLFDFVSDP LSDLKWKEVK RAALSEMVEY ITHN RNVIT EPIYPEVVHM FAVNMFRTLP PSSNPTGAEF DPEEDEPTLE AAWPHLQLVY EFFLRFLESP DFQPNIAKKY IDQKF VLQL LELFDSEDPR ERDFLKTTLH RIYGKFLGLR AYIRKQINNI FYRFIYETEH HNGIAELLEI LGSIINGFAL PLKEEH KIF LLKVLLPLHK VKSLSVYHPQ LAYCVVQFLE KDSTLTEPVV MALLKYWPKT HSPKEVMFLN ELEEILDVIE PSEFVKI ME PLFRQLAKCV SSPHFQVAER ALYYWNNEYI MSLISDNAAK ILPIMFPSLY RNSKT

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Macromolecule #3: DNA (5'-D(*AP*CP*TP*GP*TP*GP*TP*TP*TP*GP*GP*CP*GP*CP*TP*TP*CP*TP*...

MacromoleculeName: DNA (5'-D(*AP*CP*TP*GP*TP*GP*TP*TP*TP*GP*GP*CP*GP*CP*TP*TP*CP*TP*CP*TP*C)-3')
type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Simian T-lymphotropic virus 1
Molecular weightTheoretical: 9.221909 KDa
SequenceString:
(DA)(DC)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DG) (DG)(DC)(DG)(DC)(DT)(DT)(DC)(DT)(DC)(DT) (DC)(DC)(DC)(DG)(DG)(DA)(DG)(DA)(DG) (DA)

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Macromolecule #4: DNA (5'-D(*GP*AP*GP*AP*GP*AP*AP*GP*CP*GP*CP*CP*AP*AP*AP*CP*AP*CP*...

MacromoleculeName: DNA (5'-D(*GP*AP*GP*AP*GP*AP*AP*GP*CP*GP*CP*CP*AP*AP*AP*CP*AP*CP*A)-3')
type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Simian T-lymphotropic virus 1
Molecular weightTheoretical: 8.59356 KDa
SequenceString:
(DT)(DC)(DT)(DC)(DT)(DC)(DC)(DG)(DG)(DG) (DA)(DG)(DA)(DG)(DA)(DA)(DG)(DC)(DG)(DC) (DC)(DA)(DA)(DA)(DC)(DA)(DC)(DA)

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: Bictegravir

MacromoleculeName: Bictegravir / type: ligand / ID: 7 / Number of copies: 2 / Formula: KLQ
Molecular weightTheoretical: 449.38 Da
Chemical component information

ChemComp-KLQ:
Bictegravir / inhibitor*YM

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.7 mg/mL
BufferpH: 6
Component:
ConcentrationNameFormula
20.0 mMBis tris propane
0.3 MSodium chlorideNaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 240 sec.
Details: Glow-discharged for 4 min at 45 mA on an Emitech K100X instrument (Electron Microscopy Sciences) and covered with a layer of graphene oxide (Sigma-Aldrich, catalogue #763705) immediately before being used.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
DetailsComplex was isolated by size exclusion chromatography

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1714199
Startup modelType of model: NONE / Details: ab initio mask made in cryosparc
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 39731
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6z2y
PDB Unreleased entry


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: 6Z2Y was fitted into the cryoEM map using Chimera. The model was adjusted to fit the map; metal ions and drug docked into the map manually using Coot. The final model was subjected to Phenix. ...Details: 6Z2Y was fitted into the cryoEM map using Chimera. The model was adjusted to fit the map; metal ions and drug docked into the map manually using Coot. The final model was subjected to Phenix.real_space_refine using C2 NCS and secondary structure and metal ion coordination restraints.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7ouh:
Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor bictegravir

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