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- PDB-7ash: HIV-1 Gag immature lattice. GagdeltaMASP1T8I -

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Basic information

Entry
Database: PDB / ID: 7ash
TitleHIV-1 Gag immature lattice. GagdeltaMASP1T8I
ComponentsGag protein
KeywordsVIRAL PROTEIN / HIV-1 / Gag / immature lattice / SP1 / T8I
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral capsid / nucleic acid binding / host cell plasma membrane / zinc ion binding
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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
Biological speciesHuman immunodeficiency virus 1
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.2 Å
AuthorsMendonca, L. / Zhang, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust2064422/Z17/Z United Kingdom
CitationJournal: Commun Biol / Year: 2021
Title: CryoET structures of immature HIV Gag reveal six-helix bundle.
Authors: Luiza Mendonça / Dapeng Sun / Jiying Ning / Jiwei Liu / Abhay Kotecha / Mateusz Olek / Thomas Frosio / Xiaofeng Fu / Benjamin A Himes / Alex B Kleinpeter / Eric O Freed / Jing Zhou / ...Authors: Luiza Mendonça / Dapeng Sun / Jiying Ning / Jiwei Liu / Abhay Kotecha / Mateusz Olek / Thomas Frosio / Xiaofeng Fu / Benjamin A Himes / Alex B Kleinpeter / Eric O Freed / Jing Zhou / Christopher Aiken / Peijun Zhang /
Abstract: Gag is the HIV structural precursor protein which is cleaved by viral protease to produce mature infectious viruses. Gag is a polyprotein composed of MA (matrix), CA (capsid), SP1, NC (nucleocapsid), ...Gag is the HIV structural precursor protein which is cleaved by viral protease to produce mature infectious viruses. Gag is a polyprotein composed of MA (matrix), CA (capsid), SP1, NC (nucleocapsid), SP2 and p6 domains. SP1, together with the last eight residues of CA, have been hypothesized to form a six-helix bundle responsible for the higher-order multimerization of Gag necessary for HIV particle assembly. However, the structure of the complete six-helix bundle has been elusive. Here, we determined the structures of both Gag in vitro assemblies and Gag viral-like particles (VLPs) to 4.2 Å and 4.5 Å resolutions using cryo-electron tomography and subtomogram averaging by emClarity. A single amino acid mutation (T8I) in SP1 stabilizes the six-helix bundle, allowing to discern the entire CA-SP1 helix connecting to the NC domain. These structures provide a blueprint for future development of small molecule inhibitors that can lock SP1 in a stable helical conformation, interfere with virus maturation, and thus block HIV-1 infection.
History
DepositionOct 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.0Jun 23, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 23, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 23, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 23, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 23, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 23, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 23, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.3Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: Gag protein
B: Gag protein
C: Gag protein
D: Gag protein
I: Gag protein
N: Gag protein
E: Gag protein
J: Gag protein
O: Gag protein
F: Gag protein
K: Gag protein
P: Gag protein
G: Gag protein
L: Gag protein
Q: Gag protein
H: Gag protein
M: Gag protein
R: Gag protein


Theoretical massNumber of molelcules
Total (without water)462,79018
Polymers462,79018
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area61770 Å2
ΔGint-359 kcal/mol
Surface area223820 Å2
MethodPISA

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Components

#1: Protein
Gag protein


Mass: 25710.555 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Homo sapiens (human) / References: UniProt: C9DXR6
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Human immunodeficiency virus 1 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 120 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131942 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 90 / Num. of volumes extracted: 131942
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00833066
ELECTRON MICROSCOPYf_angle_d1.24244910
ELECTRON MICROSCOPYf_dihedral_angle_d28.4224446
ELECTRON MICROSCOPYf_chiral_restr0.0565040
ELECTRON MICROSCOPYf_plane_restr0.0085850

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