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- PDB-8fzc: HIV-2 Gag Capsid from Immature Virus-like Particles -

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Basic information

Entry
Database: PDB / ID: 8fzc
TitleHIV-2 Gag Capsid from Immature Virus-like Particles
ComponentsSpacer peptide 2
KeywordsVIRUS LIKE PARTICLE / Retrovirus / Lentivirus / Gag / Capsid / HIV-2 / lattice
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
: / 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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...: / 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 / 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
Biological speciesHuman immunodeficiency virus type 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsTalledge, N. / Zhang, W. / Mansky, L.M.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)124279 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118047 United States
National Science Foundation (NSF, United States)DMR-2011401 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)124165 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)007097 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)150351 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)83196 United States
CitationJournal: J Mol Biol / Year: 2023
Title: HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation.
Authors: Nathaniel Talledge / Huixin Yang / Ke Shi / Raffaele Coray / Guichuan Yu / William G Arndt / Shuyu Meng / Gloria C Baxter / Luiza M Mendonça / Daniel Castaño-Díez / Hideki Aihara / Louis ...Authors: Nathaniel Talledge / Huixin Yang / Ke Shi / Raffaele Coray / Guichuan Yu / William G Arndt / Shuyu Meng / Gloria C Baxter / Luiza M Mendonça / Daniel Castaño-Díez / Hideki Aihara / Louis M Mansky / Wei Zhang /
Abstract: Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus ...Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used the single particle cryo-electron microscopy method to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 Å resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag lattice structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 Å resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10-12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.
History
DepositionJan 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.initial_refinement_model_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spacer peptide 2
B: Spacer peptide 2
C: Spacer peptide 2


Theoretical massNumber of molelcules
Total (without water)75,3293
Polymers75,3293
Non-polymers00
Water00
1
A: Spacer peptide 2
B: Spacer peptide 2
C: Spacer peptide 2
x 6


Theoretical massNumber of molelcules
Total (without water)451,97718
Polymers451,97718
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
MethodUCSF CHIMERA

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Components

#1: Protein Spacer peptide 2 / SP2 / p1


Mass: 25109.822 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 2 (ISOLATE ROD)
Gene: gag / Variant: isolate ROD / Plasmid: pN3 / Details (production host): CMV promotor / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P04590

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human immunodeficiency virus type 2 (ISOLATE ROD) / Type: VIRUS
Details: HIV-2 VLPs generated by Gag co-overexpressed with HIV-2 Env in Hek293T cells and purified from media supernatant
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Human immunodeficiency virus type 2 (ISOLATE ROD)
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellName: Capsid / Diameter: 2100 nm
Buffer solutionpH: 8 / Details: 100 mM NaCl, 10 mM Tris-HCL pH 8.0, 1mM EDTA
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
210 mMTris-HClC4H11NO31
31 mMEthylenediaminetetraacetic acidC10H16N2O81
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Leica ACE600 Glow Discharger. / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 292.15 K / Details: Leica GP2 Grid Plunger.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2250 nm / Nominal defocus min: 750 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 10 / Num. of real images: 2508
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEMimage acquisition
4Gctf1.06CTF correction
7PHENIXmodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46017 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1 / Chain-ID: A / Pdb chain-ID: A / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-ID
12WLV

2wlv

2WLV1
25L93

5l93

5L932
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025391
ELECTRON MICROSCOPYf_angle_d0.6447323
ELECTRON MICROSCOPYf_dihedral_angle_d4.141717
ELECTRON MICROSCOPYf_chiral_restr0.042798
ELECTRON MICROSCOPYf_plane_restr0.004972

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