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- EMDB-0337: MicroED Structure of the CTD-SP1 fragment of HIV-1 Gag with bound... -

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Basic information

Entry
Database: EMDB / ID: EMD-0337
TitleMicroED Structure of the CTD-SP1 fragment of HIV-1 Gag with bound maturation inhibitor Bevirimat.
Map dataMicroED map of the CTD-SP1 fragment of HIV-1 Gag with bound maturation inhibitor Bevirimat.
Sample
  • Complex: CTD-SP1 fragment of HIV-1 Gag with bound maturation inhibitor Bevirimat
    • Protein or peptide: CTD-SP1 fragment of HIV-1 Gag
KeywordsBevirimat / HIV-1 Gag / MicroED / Immature Hexagonal Lattice / VIRAL PROTEIN
Function / homology
Function and homology information


Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / 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 ...Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / 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 / viral process / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host multivesicular body / viral capsid / viral nucleocapsid / viral translational frameshifting / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Gag protein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Methodelectron crystallography / cryo EM
AuthorsPurdy MD / Shi D
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM066087 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM128507 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
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
DepositionNov 16, 2018-
Header (metadata) releaseDec 12, 2018-
Map releaseDec 12, 2018-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0337.png

Downloads & links

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Map

FileDownload / File: emd_0337.map.gz / Format: CCP4 / Size: 402.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMicroED map of the CTD-SP1 fragment of HIV-1 Gag with bound maturation inhibitor Bevirimat.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.19 Å/pix.
x 528 pix.
= 100.478 Å		0.19 Å/pix.
x 514 pix.
= 97.814 Å		0.19 Å/pix.
x 389 pix.
= 74.027 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.1903 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-4.809102 - 7.1038866
Average (Standard dev.)-0.0016254015 (±0.9474982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-266-98-153
Dimensions514389528
Spacing528514389
CellA: 100.4784 Å / B: 97.8142 Å / C: 74.0267 Å
α: 90.0 ° / β: 95.042 ° / γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.190299242424240.190299610894940.19030077120823
M x/y/z528514389
origin x/y/z0.0000.0000.000
length x/y/z100.47897.81474.027
α/β/γ90.00095.04290.000
start NX/NY/NZ-153-266-98
NX/NY/NZ528514389
MAP C/R/S321
start NC/NR/NS-98-266-153
NC/NR/NS389514528
D min/max/mean-4.8097.104-0.002

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Supplemental data

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Sample components

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Entire : CTD-SP1 fragment of HIV-1 Gag with bound maturation inhibitor Bev...

EntireName: CTD-SP1 fragment of HIV-1 Gag with bound maturation inhibitor Bevirimat
Components
  • Complex: CTD-SP1 fragment of HIV-1 Gag with bound maturation inhibitor Bevirimat
    • Protein or peptide: CTD-SP1 fragment of HIV-1 Gag

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Supramolecule #1: CTD-SP1 fragment of HIV-1 Gag with bound maturation inhibitor Bev...

SupramoleculeName: CTD-SP1 fragment of HIV-1 Gag with bound maturation inhibitor Bevirimat
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3
Molecular weightTheoretical: 12.17387 KDa

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Macromolecule #1: CTD-SP1 fragment of HIV-1 Gag

MacromoleculeName: CTD-SP1 fragment of HIV-1 Gag / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 12.192895 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HMHHHHHHGG SPTSILDIRQ GPKEPFRDYV DRFYKTLRAE QASQEVKNWM TETLLVQNAN PDCKTILKAL GPGATLEEMM TACQGVGGP GHKARVLAEA MSQVTNTATI M

UniProtKB: Gag protein

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
0.1 MBis-Tris Propane
1.1 MLithium sulfateLiSO4
GridModel: Quantifoil R2/4 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 30 seconds each side
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Details10 microliters of 0.8 mg/ml protein was mixed with 10 microliters of a solution of 0.64 mM Bevirimat in DMSO/water.

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 5 / Average exposure time: 5.0 sec. / Average electron dose: 0.05 e/Å2
Details: Data from 5 crystals was merged for structure determination.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 2000 mm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES
Molecular replacementSoftware - Name: PHENIX (ver. dev-2747)
Merging software listSoftware - Name: AIMLESS
Crystallography statisticsNumber intensities measured: 98015 / Number structure factors: 13021 / Fourier space coverage: 83.4 / R sym: 0.544 / R merge: 0.509 / Overall phase error: 0 / Overall phase residual: 1 / Phase error rejection criteria: 0 / High resolution: 2.9 Å
Shell:
Shell IDHigh resolutionLow resolutionNumber structure factorsPhase residualFourier space coverageMultiplicity
12.9 Å19.9 Å116351.083.4000000000000067.5
22.9 Å3.0 Å11371.082.2999999999999977.5

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Atomic model buiding 1

Initial modelPDB ID:

5i4t


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 52.6
Output model

PDB-6n3u:
MicroED Structure of the CTD-SP1 fragment of HIV-1 Gag with bound maturation inhibitor Bevirimat.

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