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- EMDB-28955: Asymmetric structure of cleaved HIV-1 AE2 envelope glycoprotein t... -

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Basic information

Entry
Database: EMDB / ID: EMD-28955
TitleAsymmetric structure of cleaved HIV-1 AE2 envelope glycoprotein trimer in styrene-maleic acid lipid nanoparticles (AE2.2)
Map data
Sample
  • Complex: HIV-1 Env AE2.2
    • Protein or peptide: HIV-1 Envelop Glycoprotein
KeywordsHIV-1 / envelope glycoprotein / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 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_28955.png

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Map

FileDownload / File: emd_28955.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 160 pix.
= 264. Å		1.65 Å/pix.
x 160 pix.
= 264. Å		1.65 Å/pix.
x 160 pix.
= 264. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.029137393 - 0.096994095
Average (Standard dev.)0.0020956201 (±0.0056937947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28955_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_28955_half_map_2.map
Projections & Slices
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Sample components

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Entire : HIV-1 Env AE2.2

EntireName: HIV-1 Env AE2.2
Components
  • Complex: HIV-1 Env AE2.2
    • Protein or peptide: HIV-1 Envelop Glycoprotein

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Supramolecule #1: HIV-1 Env AE2.2

SupramoleculeName: HIV-1 Env AE2.2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 Envelop Glycoprotein

MacromoleculeName: HIV-1 Envelop Glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
SequenceString: MRVKEKYQHL WRWGWRWGTM LLGMLMICSA TEKLWVTVYY GVPVWKEATT TLFCASDAKA YDTEVHNVWA THACVPTDPN PQEVVLENVT ENFNMWKNNM VEQMHEDIIS LWDESLKPCV KLTPLCVTLN CTDLRNVTNI NNSSEGMRGE IKNCSFNITT SIKDKVKKDY ...String:
MRVKEKYQHL WRWGWRWGTM LLGMLMICSA TEKLWVTVYY GVPVWKEATT TLFCASDAKA YDTEVHNVWA THACVPTDPN PQEVVLENVT ENFNMWKNNM VEQMHEDIIS LWDESLKPCV KLTPLCVTLN CTDLRNVTNI NNSSEGMRGE IKNCSFNITT SIKDKVKKDY ALFYKLDVVP IDNDNTSYRL INCNTSTITQ ACPKVSFEPI PIHYCTPAGF AILKCKDKKF NGTGPCKNVS TVQCTHGIKP VVSTQLLLNG SLAEEEVVIR SSNFTDNAKN IIVQLKESVE INCTRPNNNT RKSIHIGPGK AFYTTGDIIG DIRQAHCNIS RTKWNNTLNQ IATKLKEQFG NNKTIVFNQS SGGDPEIVMH SFNCGGEFFY CNSTQLFNST WNFNGTWNLT QSNGTEGNDT ITLPCKIKQI INMWQEVGKA MYAPPIRGQI RCSSNITGLI LTRDGGNNHN NDTETFRPGG GDMRDNWRSE LYKYKVVKIE PLGVAPTKAK RRVVQREKRA VGTIGAMFLG FLGAAGSTMG AASITLTVQA RLLLSGIVQQ QNNLLKAIEA QQHLLKLTVW GIKQLQARVL TVERYLRDQQ LLGIWGCSGK LICTTAVPWN ASWSNKTLDM IWNNMTWMEW EKEIDNYTGL IYTLIEESQN QQEKNEKELL

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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: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 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: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21068
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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