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- EMDB-61554: Asymmetric structure of cleaved HIV-1 Tri FPPR envelope glycoprot... -

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Basic information

Entry
Database: EMDB / ID: EMD-61554
TitleAsymmetric structure of cleaved HIV-1 Tri FPPR envelope glycoprotein trimer in amphipol-lipid nanodiscs (Tri FPPR.2)
Map dataThe main map with amplitude corrected
Sample
  • Complex: HIV-1 Env Tri FPPR.2
    • Protein or peptide: Envelope glycoprotein gp160
  • 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
Keywordsviral entry / VIRAL PROTEIN
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 gp160
Similarity search - Component
Biological speciesSimian-Human immunodeficiency virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsQi Y / Zhang S / Sodroski J / Mao Y
Funding support China, United States, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12125401 China
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI124982 United States
CitationJournal: Commun Biol / Year: 2025
Title: The membrane-proximal external region of human immunodeficiency virus (HIV-1) envelope glycoprotein trimers in A18-lipid nanodiscs.
Authors: Yi Qi / Shijian Zhang / Kunyu Wang / Haitao Ding / Zhiqing Zhang / Saumya Anang / Hanh T Nguyen / John C Kappes / Joseph Sodroski / Youdong Mao /
Abstract: During human immunodeficiency virus (HIV-1) entry, the metastable pretriggered envelope glycoprotein (Env) trimer ((gp120/gp41)) opens asymmetrically. We present cryo-EM structures of cleaved ...During human immunodeficiency virus (HIV-1) entry, the metastable pretriggered envelope glycoprotein (Env) trimer ((gp120/gp41)) opens asymmetrically. We present cryo-EM structures of cleaved asymmetric Env trimers in amphipol-lipid nanodiscs. The gp41 membrane-proximal external region (MPER) could be traced in Env protomers that remained close to the nanodisc despite Env tilting. The MPER interacts with the gp120 C-termini and gp41 α9 helices at the base of the Env trimer. MPER conformation is coupled with the tilt angles of the α9 helices, the helicity of the gp41 heptad repeat (HR1) regions, and the opening angles between the protomers of the asymmetric trimers. Our structural models explain the stabilizing effects of MPER integrity and Env proteolytic maturation on the pretriggered Env conformation. Superimposed on the asymmetry of the Env protomers, variation in the glycans at the trimer apex creates substantial structural heterogeneity in the V2 quaternary epitopes of difficult-to-elicit broadly neutralizing antibodies.
History
DepositionSep 16, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61554.png

Downloads & links

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Map

FileDownload / File: emd_61554.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe main map with amplitude corrected
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 180 pix.
= 297. Å		1.65 Å/pix.
x 180 pix.
= 297. Å		1.65 Å/pix.
x 180 pix.
= 297. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.05229686 - 0.14035667
Average (Standard dev.)0.00032311297 (±0.0057511483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61554_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61554_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 Tri FPPR.2

EntireName: HIV-1 Env Tri FPPR.2
Components
  • Complex: HIV-1 Env Tri FPPR.2
    • Protein or peptide: Envelope glycoprotein gp160
  • 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 Tri FPPR.2

SupramoleculeName: HIV-1 Env Tri FPPR.2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Simian-Human immunodeficiency virus
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Simian-Human immunodeficiency virus
Molecular weightTheoretical: 82.23382 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRVKEKYQHL WRWGWRWGTM LLGMLMICSA TEKLWVTVYY GVPVWKEATT TLFCASDAKA YDTEVHNVWA THACVPTDPN PQEVVLENV TENFNMWKNN MVEQMHEDII SLWDESLKPC VKLTPLCVTL NCTDLRNVTN INNSSEGMRG EIKNCSFNIT T SIRDKVKK ...String:
MRVKEKYQHL WRWGWRWGTM LLGMLMICSA TEKLWVTVYY GVPVWKEATT TLFCASDAKA YDTEVHNVWA THACVPTDPN PQEVVLENV TENFNMWKNN MVEQMHEDII SLWDESLKPC VKLTPLCVTL NCTDLRNVTN INNSSEGMRG EIKNCSFNIT T SIRDKVKK DYALFYRLDV VPIDNDNTSY RLINCNTSTI TQACPKVSFE PIPIHYCTPA GFAILKCKDK KFNGTGPCKN VS TVQCTHG IRPVVSTQLL LNGSLAEEEV VIRSSNFTDN AKNIIVQLKE SVEINCTRPN NNTRKSIHIG PGRAFYTTGD IIG DIRQAH CNISRTKWNN TLNQIATKLK EQFGNNKTIV FNQSSGGDPE IVMHSFNCGG EFFYCNSTQL FNSTWNFNGT WNLT QSNGT EGNDTITLPC RIKQIINMWQ EVGKAMYAPP IRGQIRCSSN ITGLILTRDG GNNHNNDTET FRPGGGDMRD NWRSE LYKY KVVKIEPLGV APTKAKRRVV QREKRAVGTI GAMFLGFLGA AGSTMGVASM TLTVQARQLL SGIVQQQNNL LRAIEA QQH LLKLTVWGIK QLQARVLTVE RYLRDQQLLG IWGCSGKLIC TTAVPWNASW SNKTLDMIWN NMTWMEWERE IDNYTGL IY TLIEESQNQQ EKNEQELLEL DKWASLWNWF DITNWLWYIK IFIMIVGGLI GLRIVFTVLS IVNRVRQGYS PGGGHHHH H H

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 11 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #14: 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: 14 / 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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50646
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9jkg:
Asymmetric structure of cleaved HIV-1 Tri FPPR envelope glycoprotein trimer in amphipol-lipid nanodiscs (Tri FPPR.2)

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