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- EMDB-20483: Structure of HIV cleaved synaptic complex (CSC) intasome bound wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-20483
TitleStructure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and Bictegravir (BIC)
Map data
SampleAssembly of HIV integrase and viral DNA:
Chimeric Sso7d and HIV-1 integrase / (nucleic-acidNucleic acid) x 2 / (ligand) x 4
Function / homology
Function and homology information


endoribonuclease activity / DNA integration / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / DNA binding / zinc ion binding / cytoplasm
Integrase, catalytic core / Integrase-like, N-terminal / Integrase, C-terminal domain superfamily, retroviral / Ribonuclease H superfamily / Integrase, C-terminal, retroviral / DNA-binding 7kDa protein / Integrase, N-terminal zinc-binding domain / Ribonuclease H-like superfamily / Chromo-like domain superfamily
DNA-binding protein 7d / Integrase
Biological specieshiv (virus) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLyumkis D / Passos D
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136680 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI146017 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069832 United States
CitationJournal: Science / Year: 2020
Title: Structural basis for strand transfer inhibitor binding to HIV intasomes.
Authors: Dario Oliveira Passos / Min Li / Ilona K Jóźwik / Xue Zhi Zhao / Diogo Santos-Martins / Renbin Yang / Steven J Smith / Youngmin Jeon / Stefano Forli / Stephen H Hughes / Terrence R Burke / Robert Craigie / Dmitry Lyumkis /
Abstract: The HIV intasome is a large nucleoprotein assembly that mediates the integration of a DNA copy of the viral genome into host chromatin. Intasomes are targeted by the latest generation of ...The HIV intasome is a large nucleoprotein assembly that mediates the integration of a DNA copy of the viral genome into host chromatin. Intasomes are targeted by the latest generation of antiretrovirals, integrase (IN) strand transfer inhibitors (INSTIs). Challenges associated with lentiviral intasome biochemistry have hindered high-resolution structural studies of how INSTIs bind to their native drug target. Here, we present high-resolution cryo-electron microscopy (cryo-EM) structures of HIV intasomes bound to the latest generation INSTIs. These structures highlight how small changes in the IN active site can have significant implications for drug binding and design and provide mechanistic insights into why a leading INSTI retains efficacy against a broad spectrum of drug resistant variants. The data have implications for expanding effective treatments available for HIV-infected individuals.
Validation ReportPDB-ID: 6puw

SummaryFull reportAbout validation report
History
DepositionJul 18, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6puw
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6puw
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20483.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 384 pix.
= 303.36 Å
0.79 Å/pix.
x 384 pix.
= 303.36 Å
0.79 Å/pix.
x 384 pix.
= 303.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.79 Å
Density
Contour LevelBy AUTHOR: 3 / Movie #1: 4
Minimum - Maximum-18.486778 - 38.296665
Average (Standard dev.)0.024489356 (±0.69340193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 303.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.790.790.79
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z303.360303.360303.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-18.48738.2970.024

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Supplemental data

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Sample components

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Entire Assembly of HIV integrase and viral DNA

EntireName: Assembly of HIV integrase and viral DNA / Number of components: 8

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Component #1: protein, Assembly of HIV integrase and viral DNA

ProteinName: Assembly of HIV integrase and viral DNA / Recombinant expression: No
MassTheoretical: 400 kDa
SourceSpecies: hiv (virus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Chimeric Sso7d and HIV-1 integrase

ProteinName: Chimeric Sso7d and HIV-1 integrase / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 42.321258 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: nucleic-acid, viral DNA non-transferred strand

nucleic acidName: viral DNA non-transferred strand / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DC)(DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG) (DA)(DT)(DT)(DT)(DT)(DC)(DC)(DC)(DG)(DC) (DC)(DC)(DA)(DC)(DG)(DC)(DT)
MassTheoretical: 8.188271 kDa
SourceSpecies: Human immunodeficiency virus 1

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Component #4: nucleic-acid, viral DNA transferred strand

nucleic acidName: viral DNA transferred strand / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DG)(DC)(DG)(DT)(DG)(DG)(DG)(DC)(DG) (DG)(DG)(DA)(DA)(DA)(DA)(DT)(DC)(DT)(DC) (DT)(DA)(DG)(DC)(DA)
MassTheoretical: 7.773023 kDa
SourceSpecies: Human immunodeficiency virus 1

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Component #5: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #6: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #7: ligand, Bictegravir

LigandName: Bictegravir / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.44938 kDa

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Component #8: ligand, water

LigandName: water / Number of Copies: 156 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / pH: 6.2
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 37000 X (nominal), 63291 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2188

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 146022
3D reconstructionAlgorithm: FOURIER SPACE / Software: cisTEM / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Correlation coefficient / Refinement space: REAL
Input PDB model: 3L3U, 1K6Y, 5U1C
Output model

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