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- PDB-6vws: Hexamer of Helical HIV capsid by RASTR method -

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Basic information

Entry
Database: PDB / ID: 6vws
TitleHexamer of Helical HIV capsid by RASTR method
ComponentsHIV capsid protein
KeywordsVIRAL PROTEIN / Helical reconstruction / GS-6207 Hexamer HIV / RASTR
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane ...viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / RNA binding / zinc ion binding / membrane / cytoplasm
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) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / 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) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / 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 polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.08 Å
AuthorsZhao, H. / Iqbal, N. / Asturias, F. / Kvaratskhelia, M. / Vanblerkom, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-67167 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI062520 United States
CitationJournal: Science / Year: 2020
Title: Structural and mechanistic bases for a potent HIV-1 capsid inhibitor.
Authors: Stephanie M Bester / Guochao Wei / Haiyan Zhao / Daniel Adu-Ampratwum / Naseer Iqbal / Valentine V Courouble / Ashwanth C Francis / Arun S Annamalai / Parmit K Singh / Nikoloz Shkriabai / ...Authors: Stephanie M Bester / Guochao Wei / Haiyan Zhao / Daniel Adu-Ampratwum / Naseer Iqbal / Valentine V Courouble / Ashwanth C Francis / Arun S Annamalai / Parmit K Singh / Nikoloz Shkriabai / Peter Van Blerkom / James Morrison / Eric M Poeschla / Alan N Engelman / Gregory B Melikyan / Patrick R Griffin / James R Fuchs / Francisco J Asturias / Mamuka Kvaratskhelia /
Abstract: The potent HIV-1 capsid inhibitor GS-6207 is an investigational principal component of long-acting antiretroviral therapy. We found that GS-6207 inhibits HIV-1 by stabilizing and thereby preventing ...The potent HIV-1 capsid inhibitor GS-6207 is an investigational principal component of long-acting antiretroviral therapy. We found that GS-6207 inhibits HIV-1 by stabilizing and thereby preventing functional disassembly of the capsid shell in infected cells. X-ray crystallography, cryo-electron microscopy, and hydrogen-deuterium exchange experiments revealed that GS-6207 tightly binds two adjoining capsid subunits and promotes distal intra- and inter-hexamer interactions that stabilize the curved capsid lattice. In addition, GS-6207 interferes with capsid binding to the cellular HIV-1 cofactors Nup153 and CPSF6 that mediate viral nuclear import and direct integration into gene-rich regions of chromatin. These findings elucidate structural insights into the multimodal, potent antiviral activity of GS-6207 and provide a means for rationally developing second-generation therapies.
History
DepositionFeb 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: HIV capsid protein
B: HIV capsid protein
C: HIV capsid protein
D: HIV capsid protein
M: HIV capsid protein
N: HIV capsid protein


Theoretical massNumber of molelcules
Total (without water)147,6796
Polymers147,6796
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
HIV capsid protein


Mass: 24613.174 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: B6DRA0, UniProt: P12493*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Hexamer of helical HIV capsid protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 1M NaCl, 50mM Tris pH 8.0
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 28000 X / Calibrated magnification: 28000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 700 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 70 K
Image recordingElectron dose: 47.36 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 4246
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails
1RELION3.0.4particle selection
2Leginonimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9RELION3.0.4initial Euler assignment
10RELION3.0.4final Euler assignment3D refinement
11cryoSPARC2classification
12cryoSPARC23D reconstruction
19PHENIX3758model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 150.32 ° / Axial rise/subunit: 7.61 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 146291
Details: A total of 208,225helical segments were extracted from manually selected, well-ordered helical tubes using Relion
3D reconstructionResolution: 6.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 245050 / Algorithm: BACK PROJECTION
Details: A non-helical approach (RASTR) to calculate a volume from the same subset of data used for helical analysis. The position and rotation to the center of a single hexamer in the final helical ...Details: A non-helical approach (RASTR) to calculate a volume from the same subset of data used for helical analysis. The position and rotation to the center of a single hexamer in the final helical volume was determined and used along the final refined helical rise and twist to extract a total of 245050 unique particles from which surrounding tube density was subtracted by reprojection using Relion. The resulting stack of 245050 particles, each extracted into a 192 multiple 192 pixel box centered around the chosen asymmetric unit for each subtracted volume, was imported into Cryosparc. 2D clustering and ab-initio heterogeneous reconstruction with 4 volumes were then used to select a subset of 96392 particle images. These images, along with the cleanest reference from ab-initio volume determination were then used to obtain a volume through 3D Refinement.
Num. of class averages: 96392 / Symmetry type: HELICAL
Atomic model buildingB value: 204.64 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6VKV

6vkv


Pdb chain-ID: A / Accession code: 6VKV / Pdb chain residue range: 1-220 / Source name: PDB / Type: experimental model

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