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- EMDB-51769: Mature HIV-1 matrix from MA-SP1 cleavage mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-51769
TitleMature HIV-1 matrix from MA-SP1 cleavage mutant
Map dataSharpened map of the mature HIV matrix solved from the virion of the HIV-1 MA-SP1 cleavage mutant.
Sample
  • Virus: HIV-1 vector pNL4-3 (others)
    • Complex: HIV-1 mature matrix
      • Protein or peptide: Gag polyprotein
      • Protein or peptide: Gag polyprotein
KeywordsHIV-1 / HIV / matrix / mature / spacer peptide 2 / SP2 / VIRAL PROTEIN
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding ...viral budding via host ESCRT complex / ISG15 antiviral mechanism / 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 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 / Retrovirus capsid, C-terminal ...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 / 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 speciesHIV-1 vector pNL4-3 (others) / Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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
Citation
Journal: Nature / Year: 2025
Title: The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation.
Authors: Stacey JCV / Hrebik D / Nand E / Shetty SD / Qu K / Boicu M / Anders-Osswein M / Uchil PD / Dick RA / Mothes W / Krausslich HG / Muller B / Briggs JAG
#1: Journal: Biorxiv / Year: 2024
Title: The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation.
Authors: Stacey JCV / Hrebik D / Nand E / Shetty SD / Qu K / Boicu M / Anders-Osswein M / Dick RA / Mothes W / Krausslich HG / Muller B / Briggs JAG
History
DepositionOct 10, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_51769.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of the mature HIV matrix solved from the virion of the HIV-1 MA-SP1 cleavage mutant.
Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.3631687 - 2.2647994
Average (Standard dev.)-0.00377327 (±0.03979854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 486.4 Å
α=β=γ: 90.0 °

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Supplemental data

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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 mature matrix
      • Protein or peptide: Gag polyprotein
      • 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 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: 82 MDa
Virus shellShell ID: 1 / Name: Gag / Diameter: 1200.0 Å

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Supramolecule #2: HIV-1 mature matrix

SupramoleculeName: HIV-1 mature matrix / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Details: HIV-1 mature matrix as a part of the MA-SP1 polypeptide, in a complex with SP2
Source (natural)Organism: HIV-1 vector pNL4-3 (others)

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Macromolecule #1: Gag polyprotein

MacromoleculeName: Gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Molecular weightTheoretical: 14.734616 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GARASVLSGG ELDKWEKIRL RPGGKKQYKL KHIVWASREL ERFAVNPGLL ETSEGCRQIL GQLQPSLQTG SEELRSLYNT IAVLYCVHQ RIDVKDTKEA LDKIEEEQNK SKKKAQQAAA DTGNNSQVSQ NY

UniProtKB: Gag polyprotein

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Macromolecule #2: Gag polyprotein

MacromoleculeName: Gag polyprotein / type: protein_or_peptide / ID: 2 / Details: spacer peptide 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Molecular weightTheoretical: 1.845154 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
FLGKIWPSHK GRPGNF

UniProtKB: Gag polyprotein

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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 MA-SP1 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: 14222 / 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: 4.5 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: 5704512
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:

13088

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 5486693
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: 6 / Avg.num./class: 210000 / Software - Name: cryoSPARC (ver. 4.3)
Details: particle stack after 2D classification was split into 4 independent subsets and each subset was classified independently

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Atomic model buiding 1

Initial modelPDB ID:

2h3i


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 52.49 / Target criteria: cross-correlation
Output model

PDB-9h1p:
Mature HIV-1 matrix from MA-SP1 cleavage mutant

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