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- EMDB-28953: Asymmetric structure of cleaved HIV-1 AD8 envelope glycoprotein t... -

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Basic information

Entry
Database: EMDB / ID: EMD-28953
TitleAsymmetric structure of cleaved HIV-1 AD8 envelope glycoprotein trimer in styrene-maleic acid lipid nanoparticles
Map data
Sample
  • Complex: HIV-1 Env AD8
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione
KeywordsHIV-1 / envelope glycoprotein / VIRAL PROTEIN
Function / homology
Function and homology information


: / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response ...: / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsWang K / Zhang S / Sodroski J / Mao Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150471 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI125093 United States
CitationJournal: Commun Biol / Year: 2023
Title: Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles.
Authors: Kunyu Wang / Shijian Zhang / Eden P Go / Haitao Ding / Wei Li Wang / Hanh T Nguyen / John C Kappes / Heather Desaire / Joseph Sodroski / Youdong Mao /
Abstract: During virus entry, the pretriggered human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer initially transits into a default intermediate state (DIS) that remains structurally ...During virus entry, the pretriggered human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer initially transits into a default intermediate state (DIS) that remains structurally uncharacterized. Here, we present cryo-EM structures at near-atomic resolution of two cleaved full-length HIV-1 Env trimers purified from cell membranes in styrene-maleic acid lipid nanoparticles without antibodies or receptors. The cleaved Env trimers exhibited tighter subunit packing than uncleaved trimers. Cleaved and uncleaved Env trimers assumed remarkably consistent yet distinct asymmetric conformations, with one smaller and two larger opening angles. Breaking conformational symmetry is allosterically coupled with dynamic helical transformations of the gp41 N-terminal heptad repeat (HR1) regions in two protomers and with trimer tilting in the membrane. The broken symmetry of the DIS potentially assists Env binding to two CD4 receptors-while resisting antibody binding-and promotes extension of the gp41 HR1 helical coiled-coil, which relocates the fusion peptide closer to the target cell membrane.
History
DepositionNov 26, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28953.png

Downloads & links

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Map

FileDownload / File: emd_28953.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.37 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.047695138 - 0.112601705
Average (Standard dev.)0.0012791681 (±0.006389841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 230.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28953_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28953_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 Env AD8

EntireName: HIV-1 Env AD8
Components
  • Complex: HIV-1 Env AD8
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione

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Supramolecule #1: HIV-1 Env AD8

SupramoleculeName: HIV-1 Env AD8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Transmembrane protein gp41

MacromoleculeName: Transmembrane protein gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 15.674881 KDa
Recombinant expressionOrganism: homo sapiens (human)
SequenceString:
LGFLGAAGST MGAASITLTV QARLLLSGIV QQQNNLLRAI EAQQHLLQLT VWGIKQLQAR VLAVERYLRD QQLLGIWGCS GKLICTTAV PWNASWSNKT LDMIWNNMTW MEWEREIDNY TGLIYTLIEE SQNQQEKNE

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Macromolecule #2: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.779613 KDa
Recombinant expressionOrganism: homo sapiens (human)
SequenceString: KLWVTVYYGV PVWKEATTTL FCASDAKAYD TEVHNVWATH ACVPTDPNPQ EVVLENVTEN FNMWKNNMVE QMHEDIISLW DQSLKPCVK LTPLCVTLNC TDLRNVTNIN NSSEGMRGEI KNCSFNITTS IRDKVKKDYA LFYRLDVVPI DNDNTSYRLI N CNTSTITQ ...String:
KLWVTVYYGV PVWKEATTTL FCASDAKAYD TEVHNVWATH ACVPTDPNPQ EVVLENVTEN FNMWKNNMVE QMHEDIISLW DQSLKPCVK LTPLCVTLNC TDLRNVTNIN NSSEGMRGEI KNCSFNITTS IRDKVKKDYA LFYRLDVVPI DNDNTSYRLI N CNTSTITQ ACPKVSFEPI PIHYCTPAGF AILKCKDKKF NGTGPCKNVS TVQCTHGIRP VVSTQLLLNG SLAEEEVVIR SS NFTDNAK NIIVQLKESV EINCTRPNNN TRKSIHIGPG RAFYTTGDII GDIRQAHCNI SRTKWNNTLN QIATKLKEQF GNN KTIVFN QSSGGDPEIV MHSFNCGGEF FYCNSTQLFN STWNFNGTWN LTQSNGTEGN DTITLPCRIK QIINMWQEVG KAMY APPIR GQIRCSSNIT GLILTRDGGN NHNNDTETFR PGGGDMRDNW RSELYKYKVV KIEPLGVAPT KAKR

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 22 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #11: 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-...

MacromoleculeName: 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione
type: ligand / ID: 11 / Number of copies: 3 / Formula: 83G
Molecular weightTheoretical: 406.434 Da
Chemical component information

ChemComp-83G:
1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7n6u

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 365824
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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