+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-0335 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | MicroED Structure of the CTD-SP1 fragment of HIV-1 Gag | |||||||||||||||
![]() | Electron crystallographic map from 3D crystals (MicroED) of a CTD-SP1 fragment of HIV-1 Gag. | |||||||||||||||
![]() |
| |||||||||||||||
![]() | Bevirimat / HIV-1 Gag / MicroED / Immature Hexagonal Lattice / VIRAL PROTEIN | |||||||||||||||
Function / homology | ![]() host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / Membrane binding and targetting of GAG proteins / viral process / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host multivesicular body / viral capsid / viral nucleocapsid / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | electron crystallography / cryo EM / Resolution: 3.0 Å | |||||||||||||||
![]() | Purdy MD / Shi D | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat. Authors: Michael D Purdy / Dan Shi / Jakub Chrustowicz / Johan Hattne / Tamir Gonen / Mark Yeager / ![]() Abstract: HIV-1 protease (PR) cleavage of the Gag polyprotein triggers the assembly of mature, infectious particles. Final cleavage of Gag occurs at the junction helix between the capsid protein CA and the SP1 ...HIV-1 protease (PR) cleavage of the Gag polyprotein triggers the assembly of mature, infectious particles. Final cleavage of Gag occurs at the junction helix between the capsid protein CA and the SP1 spacer peptide. Here we used MicroED to delineate the binding interactions of the maturation inhibitor bevirimat (BVM) using very thin frozen-hydrated, 3D microcrystals of a CTD-SP1 Gag construct with and without bound BVM. The 2.9-Å MicroED structure revealed that a single BVM molecule stabilizes the six-helix bundle via both electrostatic interactions with the dimethylsuccinyl moiety and hydrophobic interactions with the pentacyclic triterpenoid ring. These results provide insight into the mechanism of action of BVM and related maturation inhibitors that will inform further drug discovery efforts. This study also demonstrates the capabilities of MicroED for structure-based drug design. | |||||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 25.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 14.3 KB 14.3 KB | Display Display | ![]() |
Images | ![]() | 107.7 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Filedesc structureFactors | ![]() | 547.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n3jMC ![]() 0337C ![]() 6n3uC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Electron crystallographic map from 3D crystals (MicroED) of a CTD-SP1 fragment of HIV-1 Gag. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.45712 Å / Y: 0.44928 Å / Z: 0.47463 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : CTD-SP1 fragment of HIV-1 Gag
Entire | Name: CTD-SP1 fragment of HIV-1 Gag |
---|---|
Components |
|
-Supramolecule #1: CTD-SP1 fragment of HIV-1 Gag
Supramolecule | Name: CTD-SP1 fragment of HIV-1 Gag / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.17387 KDa |
-Macromolecule #1: CTD-SP1 fragment of HIV-1 Gag
Macromolecule | Name: CTD-SP1 fragment of HIV-1 Gag / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.192895 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: HMHHHHHHGG SPTSILDIRQ GPKEPFRDYV DRFYKTLRAE QASQEVKNWM TETLLVQNAN PDCKTILKAL GPGATLEEMM TACQGVGGP GHKARVLAEA MSQVTNTATI M UniProtKB: Gag protein |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | electron crystallography |
Aggregation state | 3D array |
-
Sample preparation
Concentration | 0.8 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7 Component:
| |||||||||
Grid | Model: Quantifoil R2/4 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: Glow discharge 30s each side | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 6 / Average exposure time: 8.0 sec. / Average electron dose: 0.05 e/Å2 Details: Data from 6 crystals was merged for structure determination. |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 2000 mm |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
-
Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular replacement | Software - Name: PHENIX (ver. dev-2747) | |||||||||||||||||||||
Merging software list | Software - Name: AIMLESS | |||||||||||||||||||||
Crystallography statistics | Number intensities measured: 10480 / Number structure factors: 10480 / Fourier space coverage: 79.8 / R sym: 0.255 / R merge: 0.564 / Overall phase error: 0 / Overall phase residual: 1 / Phase error rejection criteria: 0 / High resolution: 3.0 Å Shell:
|