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- EMDB-16493: cryo-EM structure of BG505 SOSIP.664 HIV-1 Env trimer in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16493
Titlecryo-EM structure of BG505 SOSIP.664 HIV-1 Env trimer in complex with bNAbs EPTC112 and 3BNC117
Map dataOverall cryo-EM map of BG505 SOSIP.664 HIV-1 Env trimer in complex with bNAbs EPTC112 and 3BNC117
Sample
  • Complex: Ternary complex of Bg505 Sosip.664 HIV-1 Env with bNAbs EPTC112 and 3BNC117
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Gp41 Bg505 T332n Sosip.664
    • Protein or peptide: IgG EPTC112 Fab fragment heavy chain
    • Protein or peptide: IgG 3BNC117 Fab heavy chain
    • Protein or peptide: IgG 3BNC117 Fab Light Chain
    • Protein or peptide: IgG EPTC112 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV / post-treatment controller / broadly neutralizing antibodies / V3-site / IMMUNE SYSTEM
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 speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBaquero E / Molinos-Albert L / Mouquet H
Funding support France, United States, 3 items
OrganizationGrant numberCountry
Agence Nationale de Recherches Sur le Sida et les Hepatites Virales (ANRS)(AO2013-2 #13553 France
Agence Nationale de la Recherche (ANR)ANR-10-LABX-69-01 France
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI131365 United States
CitationJournal: Cell Host Microbe / Year: 2023
Title: Anti-V1/V3-glycan broadly HIV-1 neutralizing antibodies in a post-treatment controller.
Authors: Luis M Molinos-Albert / Eduard Baquero / Mélanie Bouvin-Pley / Valérie Lorin / Caroline Charre / Cyril Planchais / Jordan D Dimitrov / Valérie Monceaux / Matthijn Vos / / Laurent ...Authors: Luis M Molinos-Albert / Eduard Baquero / Mélanie Bouvin-Pley / Valérie Lorin / Caroline Charre / Cyril Planchais / Jordan D Dimitrov / Valérie Monceaux / Matthijn Vos / / Laurent Hocqueloux / Jean-Luc Berger / Michael S Seaman / Martine Braibant / Véronique Avettand-Fenoël / Asier Sáez-Cirión / Hugo Mouquet /
Abstract: HIV-1 broadly neutralizing antibodies (bNAbs) can decrease viremia but are usually unable to counteract autologous viruses escaping the antibody pressure. Nonetheless, bNAbs may contribute to natural ...HIV-1 broadly neutralizing antibodies (bNAbs) can decrease viremia but are usually unable to counteract autologous viruses escaping the antibody pressure. Nonetheless, bNAbs may contribute to natural HIV-1 control in individuals off antiretroviral therapy (ART). Here, we describe a bNAb B cell lineage elicited in a post-treatment controller (PTC) that exhibits broad seroneutralization and show that a representative antibody from this lineage, EPTC112, targets a quaternary epitope in the glycan-V3 loop supersite of the HIV-1 envelope glycoprotein. The cryo-EM structure of EPTC112 complexed with soluble BG505 SOSIP.664 envelope trimers revealed interactions with N301- and N156-branched N-glycans and the GDIR V3 loop motif. Although the sole contemporaneous virus circulating in this PTC was resistant to EPTC112, it was potently neutralized by autologous plasma IgG antibodies. Our findings illuminate how cross-neutralizing antibodies can alter the HIV-1 infection course in PTCs and may control viremia off-ART, supporting their role in functional HIV-1 cure strategies.
History
DepositionJan 21, 2023-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16493.png

Downloads & links

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Map

FileDownload / File: emd_16493.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall cryo-EM map of BG505 SOSIP.664 HIV-1 Env trimer in complex with bNAbs EPTC112 and 3BNC117
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å		0.86 Å/pix.
x 400 pix.
= 344. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.373852 - 4.0128746
Average (Standard dev.)-0.0021530834 (±0.08021567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local refined cryo-EM map of first bNAbs EPTC112...

Fileemd_16493_additional_1.map
AnnotationLocal refined cryo-EM map of first bNAbs EPTC112 bound to BG505 SOSIP.664 HIV-1 Env trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refined cryo-EM map of second bNAbs EPTC112...

Fileemd_16493_additional_2.map
AnnotationLocal refined cryo-EM map of second bNAbs EPTC112 bound to BG505 SOSIP.664 HIV-1 Env trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half cryo-EM map A of BG505 SOSIP.664 HIV-1...

Fileemd_16493_half_map_1.map
AnnotationHalf cryo-EM map A of BG505 SOSIP.664 HIV-1 Env trimer in complex with bNAbs EPTC112 and 3BNC117
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half cryo-EM map B of BG505 SOSIP.664 HIV-1...

Fileemd_16493_half_map_2.map
AnnotationHalf cryo-EM map B of BG505 SOSIP.664 HIV-1 Env trimer in complex with bNAbs EPTC112 and 3BNC117
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of Bg505 Sosip.664 HIV-1 Env with bNAbs EPTC112 a...

EntireName: Ternary complex of Bg505 Sosip.664 HIV-1 Env with bNAbs EPTC112 and 3BNC117
Components
  • Complex: Ternary complex of Bg505 Sosip.664 HIV-1 Env with bNAbs EPTC112 and 3BNC117
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Gp41 Bg505 T332n Sosip.664
    • Protein or peptide: IgG EPTC112 Fab fragment heavy chain
    • Protein or peptide: IgG 3BNC117 Fab heavy chain
    • Protein or peptide: IgG 3BNC117 Fab Light Chain
    • Protein or peptide: IgG EPTC112 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of Bg505 Sosip.664 HIV-1 Env with bNAbs EPTC112 a...

SupramoleculeName: Ternary complex of Bg505 Sosip.664 HIV-1 Env with bNAbs EPTC112 and 3BNC117
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Details: Gp120 Bg505 Sosip.664 T332n / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.5515 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LWVTVYYGVP VWKDAETTLF CASDAKAYET EKHNVWATHA CVPTDPNPQE IHLENVTEEF NMWKNNMVEQ MHTDIISLWD QSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN MTTELRDKKQ KVYSLFYRLD VVQINENQGN RSNNSNKEYR L INCNTSAI ...String:
LWVTVYYGVP VWKDAETTLF CASDAKAYET EKHNVWATHA CVPTDPNPQE IHLENVTEEF NMWKNNMVEQ MHTDIISLWD QSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN MTTELRDKKQ KVYSLFYRLD VVQINENQGN RSNNSNKEYR L INCNTSAI TQACPKVSFE PIPIHYCAPA GFAILKCKDK KFNGTGPCPS VSTVQCTHGI KPVVSTQLLL NGSLAEEEVM IR SENITNN AKNILVQFNT PVQINCTRPN NNTRKSIRIG PGQAFYATGD IIGDIRQAHC NVSKATWNET LGKVVKQLRK HFG NNTIIR FANSSGGDLE VTTHSFNCGG EFFYCNTSGL FNSTWISNTS VQGSNSTGSN DSITLPCRIK QIINMWQRIG QAMY APPIQ GVIRCVSNIT GLILTRDGGS TNSTTETFRP GGGDMRDNWR SELYKYKVVK IEPLGVAPTR CKRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Gp41 Bg505 T332n Sosip.664

MacromoleculeName: Gp41 Bg505 T332n Sosip.664 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 16.431627 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LGFLGAAGST MGAASMTLTV QARNLLSGIV QQQSNLLRAP EAQQHLLKLT VWGIKQLQAR VLAVERYLRD QQLLGIWGCS GKLICCTNV PWNSSWSNRN LSEIWDNMTW LQWDKEISNY TQIIYGLLEE SQNQQEKNEQ DLLALD

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Macromolecule #3: IgG EPTC112 Fab fragment heavy chain

MacromoleculeName: IgG EPTC112 Fab fragment heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.320389 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLLESGPG LVRPSETLTL TCSVFNSRVS GYYYSWIRQP PGRGLEWIAS THFSLRPSRN PSLLSRVTTS IDTERYQVFL NMRSVTAAD TAVYFCARGD ASGWRADYFP HWGQGTLVVV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QVQLLESGPG LVRPSETLTL TCSVFNSRVS GYYYSWIRQP PGRGLEWIAS THFSLRPSRN PSLLSRVTTS IDTERYQVFL NMRSVTAAD TAVYFCARGD ASGWRADYFP HWGQGTLVVV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSCDKTH HHHHH

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Macromolecule #4: IgG 3BNC117 Fab heavy chain

MacromoleculeName: IgG 3BNC117 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.640484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLLQSGAA VTKPGASVRV SCEASGYNIR DYFIHWWRQA PGQGLQWVGW INPKTGQPNN PRQFQGRVSL TRHASWDFDT FSFYMDLKA LRSDDTAVYF CARQRSDYWD FDVWGSGTQV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QVQLLQSGAA VTKPGASVRV SCEASGYNIR DYFIHWWRQA PGQGLQWVGW INPKTGQPNN PRQFQGRVSL TRHASWDFDT FSFYMDLKA LRSDDTAVYF CARQRSDYWD FDVWGSGTQV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSC

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Macromolecule #5: IgG 3BNC117 Fab Light Chain

MacromoleculeName: IgG 3BNC117 Fab Light Chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.022658 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDTVT ITCQANGYLN WYQQRRGKAP KLLIYDGSKL ERGVPSRFSG RRWGQEYNLT INNLQPEDIA TYFCQVYEF VVPGTRLDLK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD S KDSTYSLS ...String:
DIQMTQSPSS LSASVGDTVT ITCQANGYLN WYQQRRGKAP KLLIYDGSKL ERGVPSRFSG RRWGQEYNLT INNLQPEDIA TYFCQVYEF VVPGTRLDLK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD S KDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #6: IgG EPTC112 Fab Light Chain

MacromoleculeName: IgG EPTC112 Fab Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.680932 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSA SGSPGQSVTI SCTGTSSDIG ASDYVSWYQQ YPGEAPKVII YDVTKRPSGV PDRFSGSKSG TTASLTVSGL QAEDEADYY CSSDAGRHTL LFGGGTKVTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSVLTQPPSA SGSPGQSVTI SCTGTSSDIG ASDYVSWYQQ YPGEAPKVII YDVTKRPSGV PDRFSGSKSG TTASLTVSGL QAEDEADYY CSSDAGRHTL LFGGGTKVTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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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: 24 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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: 7.5 / Details: PBS
GridModel: EMS Lacey Carbon / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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:

5v8m

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 251591
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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