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- EMDB-52229: Immature HIV-1 matrix -

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Basic information

Entry
Database: EMDB / ID: EMD-52229
TitleImmature HIV-1 matrix
Map dataB-factor sharpened map
Sample
  • Virus: HIV-1 vector pNL4-3 (others)
    • Complex: HIV-1 immature matrix
      • Protein or peptide: Gag polyprotein
KeywordsHIV-1 / HIV / matrix / immature / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1 / HIV-1 vector pNL4-3 (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.83 Å
AuthorsStacey JCV / Hrebik D / Briggs JAG
Funding support Germany, United States, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)240245660 - SFB 1129 (project 5 HGK, project 6 BM, project 931 21 JAGB) Germany
German Research Foundation (DFG)DFG KR 906/7-1 (HGK) Germany
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI055403 United States
Max Planck Society Germany
CitationJournal: Nature / Year: 2025
Title: The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation.
Authors: James C V Stacey / Dominik Hrebík / Elizabeth Nand / Snehith Dyavari Shetty / Kun Qu / Marius Boicu / Maria Anders-Össwein / Pradeep D Uchil / Robert A Dick / Walther Mothes / Hans-Georg ...Authors: James C V Stacey / Dominik Hrebík / Elizabeth Nand / Snehith Dyavari Shetty / Kun Qu / Marius Boicu / Maria Anders-Össwein / Pradeep D Uchil / Robert A Dick / Walther Mothes / Hans-Georg Kräusslich / Barbara Müller / John A G Briggs /
Abstract: The virus particles of human immunodeficiency virus type 1 (HIV-1) are released in an immature, non-infectious form. Proteolytic cleavage of the main structural polyprotein Gag into functional ...The virus particles of human immunodeficiency virus type 1 (HIV-1) are released in an immature, non-infectious form. Proteolytic cleavage of the main structural polyprotein Gag into functional domains induces rearrangement into mature, infectious virions. In immature virus particles, the Gag membrane-binding domain, MA, forms a hexameric protein lattice that undergoes structural transition, following cleavage, into a distinct, mature MA lattice. The mechanism of MA lattice maturation is unknown. Here we show that released spacer peptide 2 (SP2), a conserved peptide of unknown function situated about 300 residues downstream of MA, binds MA to induce structural maturation. By high-resolution in-virus structure determination of MA, we show that MA does not bind lipid into a side pocket as previously thought, but instead binds SP2 as an integral part of the protein-protein interfaces that stabilize the mature lattice. Analysis of Gag cleavage site mutants showed that SP2 release is required for MA maturation, and we demonstrate that SP2 is sufficient to induce maturation of purified MA on lipid monolayers in vitro. SP2-triggered MA maturation correlated with faster fusion of virus with target cells. Our results reveal a new, unexpected interaction between two HIV-1 components, provide a high-resolution structure of mature MA, establish the trigger of MA structural maturation and assign function to the SP2 peptide.
History
DepositionDec 3, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52229.png

Downloads & links

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Map

FileDownload / File: emd_52229.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.9 Å/pix.
x 256 pix.
= 486.4 Å		1.9 Å/pix.
x 256 pix.
= 486.4 Å		1.9 Å/pix.
x 256 pix.
= 486.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-2.8179176 - 3.7655287
Average (Standard dev.)-0.0030559865 (±0.15516809)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 486.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52229_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: Unsharpened map

Fileemd_52229_additional_1.map
AnnotationUnsharpened map
Projections & Slices
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Half map: Half map 2

Fileemd_52229_half_map_1.map
AnnotationHalf map 2
Projections & Slices
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Half map: Half map 1

Fileemd_52229_half_map_2.map
AnnotationHalf map 1
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AxesZYX

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Sample components

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Entire : HIV-1 vector pNL4-3

EntireName: HIV-1 vector pNL4-3 (others)
Components
  • Virus: HIV-1 vector pNL4-3 (others)
    • Complex: HIV-1 immature matrix
      • Protein or peptide: Gag polyprotein

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Supramolecule #1: HIV-1 vector pNL4-3

SupramoleculeName: HIV-1 vector pNL4-3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: HEK293T cells were transfected with pcHIV with inactive viral protease which was expressed and purified.
NCBI-ID: 151458 / Sci species name: HIV-1 vector pNL4-3 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14 KDa
Virus shellShell ID: 1 / Name: Gag / Diameter: 1200.0 Å

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Supramolecule #2: HIV-1 immature matrix

SupramoleculeName: HIV-1 immature matrix / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Details: HIV-1 immature matrix as a part of the Gag polypeptide

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Macromolecule #1: Gag polyprotein

MacromoleculeName: Gag polyprotein / type: protein_or_peptide / ID: 1 / Details: HIV matrix / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GARASVLSGG ELDKWEKIRL RPGGKKQYKL KHIVWASREL ERFAVNPGLL ETSEGCRQIL GQLQPSLQTG SEELRSLYNT IAVLYCVHQ RIDVKDTKEA LDKIEEEQNK SKKKAQQAAA DTGNNSQVSQ NY

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
8.1 mmol/LNa2HPO4disodium hydrogen phosphate
1.5 mmol/LKH2PO4potassium dihydrogen phosphate
137.0 mmol/LNaClsodium chloride
2.7 mmol/LKClpotassium chloride

Details: PBS
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: LEICA EM GP
Detailspurified HIV-1 PR- particles in PBS

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 88.0 K / Max: 93.0 K
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 9942 / Average exposure time: 4.0 sec. / Average electron dose: 40.0 e/Å2 / Details: EER mode
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.1 µm / Calibrated defocus min: 0.45 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3568755
Details: A new model was trained in crYOLO using a training dataset annotated in a randomly selected set of 50-100 micrographs. Annotation was performed in the crYOLO boxmanager GUI placing positions ...Details: A new model was trained in crYOLO using a training dataset annotated in a randomly selected set of 50-100 micrographs. Annotation was performed in the crYOLO boxmanager GUI placing positions all over the visible surface of an HIV virus particle. The picks did not distinguish individual proteins or membranes.
Startup modelType of model: EMDB MAP
EMDB ID:

13087

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 5.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 174245
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final 3D classificationNumber classes: 10 / Avg.num./class: 91209 / Software - Name: cryoSPARC (ver. 4.3) / Details: 3D classification without alignment in cryosparc
FSC plot (resolution estimation)

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