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- EMDB-70475: HIV-1 Env BG505 SOSIP.664-His in complex with PGT122 and 3BNC117 Fabs -

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Entry
Database: EMDB / ID: EMD-70475
TitleHIV-1 Env BG505 SOSIP.664-His in complex with PGT122 and 3BNC117 Fabs
Map datasharpened map
Sample
  • Complex: HIV-1 Env BG505 SOSIP.664-His in complex with PGT122 and 3BNC117 Fabs
    • Protein or peptide: 3BNC117 Fab heavy chain
    • Protein or peptide: 3BNC117 Fab light chain
    • Protein or peptide: PGT122 Fab heavy chain
    • Protein or peptide: PGT122 Fab light chain
    • Protein or peptide: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120
    • Protein or peptide: Envelope glycoprotein gp160
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsbroadly neutralizing antibody / gp140 / vaccine design / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / 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 / symbiont entry into host cell ...membrane fusion involved in viral entry into host cell / 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 / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsAndrade TG / Ozorowski G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: J Virol / Year: 2025
Title: A modification to heptad repeat 1 of gp41 improves yield and/or quality of soluble pre-fusion HIV-1 envelope glycoprotein trimers.
Authors: Devidas N Chaturbhuj / Kwinten Sliepen / Albert Cupo / Benjamin Steinberg / Simon Kazimierczyk / Tarek Munawar / Kyle Kramer / Anila Yasmeen / Thales G Andrade / Wen-Hsin Lee / Lara van der ...Authors: Devidas N Chaturbhuj / Kwinten Sliepen / Albert Cupo / Benjamin Steinberg / Simon Kazimierczyk / Tarek Munawar / Kyle Kramer / Anila Yasmeen / Thales G Andrade / Wen-Hsin Lee / Lara van der Maas / Grace Gibson / Oscar Feliciano / Ivan Del Moral Sanchez / Edith Schermer / Rhianna Bronson / Alison Benner / Madhu Prabhakaran / Rosemarie Mason / P J Klasse / Andrew B Ward / Gabriel Ozorowski / Rogier W Sanders / John P Moore /
Abstract: Native-like HIV-1 envelope glycoprotein (Env) trimers, exemplified by the SOSIP design, are widely used as immunogens, analytical antigens, and for structural studies. These vaccine research and ...Native-like HIV-1 envelope glycoprotein (Env) trimers, exemplified by the SOSIP design, are widely used as immunogens, analytical antigens, and for structural studies. These vaccine research and development programs require trimers that are based on multiple HIV-1 genotypes. While a wide range of protein engineering strategies can produce SOSIP trimers from most Env gene sequences, there are still examples of trimers that are expressed only at impractically low yields or that are unstable. Accordingly, additional protein modifications aimed at overcoming such limitations need to be evaluated. Here, we describe a new heptad repeat 1 modification of gp41, known as dPG, that helps to further stabilize the gp41 component of prototypic and germline-targeting SOSIP trimers in the pre-fusion state and thereby increases post-purification yields substantially. The dPG modification involves a deletion (d) at the highly conserved 566 position that disrupts the heptad repeat and introduces proline (P) and glycine (G) substitutions at positions 567 and 568, respectively. We show that the dPG strategy reinforces previously described stabilization changes in existing SOSIP trimers and can rescue otherwise problematic trimer constructs. The latter includes trimers used to target or analyze human germline antibodies and others derived from the global HIV-1 neutralization panel. In summary, the dPG modification strategy can increase the yield and/or quality of Env trimers that are otherwise difficult to produce.
IMPORTANCE: Stabilized, soluble, pre-fusion SOSIP trimers are widely used in HIV-1 Env vaccine research. Protein engineering techniques have identified multiple ways to stabilize SOSIP trimers from a ...IMPORTANCE: Stabilized, soluble, pre-fusion SOSIP trimers are widely used in HIV-1 Env vaccine research. Protein engineering techniques have identified multiple ways to stabilize SOSIP trimers from a range of genotypes. However, some SOSIP trimers remain difficult to express at adequate yields and/or purity, so there is a need for additional modifications. Here, we identified a sequence change, designated dPG, to the gp41 subunit that increases the yield and/or quality of various otherwise problematic SOSIP trimers without compromising their antigenicity or structure. This new modification may have general value for HIV-1 vaccine research and development.
History
DepositionMay 1, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70475.png

Downloads & links

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Map

FileDownload / File: emd_70475.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 560 pix.
= 406. Å		0.73 Å/pix.
x 560 pix.
= 406. Å		0.73 Å/pix.
x 560 pix.
= 406. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.5081919 - 0.848329
Average (Standard dev.)0.00010999 (±0.015426042)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 406.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70475_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: half map B

Fileemd_70475_half_map_1.map
Annotationhalf map B
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_70475_half_map_2.map
Annotationhalf map A
Projections & Slices
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Sample components

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Entire : HIV-1 Env BG505 SOSIP.664-His in complex with PGT122 and 3BNC117 Fabs

EntireName: HIV-1 Env BG505 SOSIP.664-His in complex with PGT122 and 3BNC117 Fabs
Components
  • Complex: HIV-1 Env BG505 SOSIP.664-His in complex with PGT122 and 3BNC117 Fabs
    • Protein or peptide: 3BNC117 Fab heavy chain
    • Protein or peptide: 3BNC117 Fab light chain
    • Protein or peptide: PGT122 Fab heavy chain
    • Protein or peptide: PGT122 Fab light chain
    • Protein or peptide: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120
    • Protein or peptide: Envelope glycoprotein gp160
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Env BG505 SOSIP.664-His in complex with PGT122 and 3BNC117 Fabs

SupramoleculeName: HIV-1 Env BG505 SOSIP.664-His in complex with PGT122 and 3BNC117 Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: 3BNC117 Fab heavy chain

MacromoleculeName: 3BNC117 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.656484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLLQSGAA VTKPGASVRV SCEASGYNIR DYFIHWWRQA PGQGLQWVGW INPKTGQPNN PRQFQGRVSL TRHASWDFDT YSFYMDLKA LRSDDTAVYF CARQRSDYWD FDVWGSGTQV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QVQLLQSGAA VTKPGASVRV SCEASGYNIR DYFIHWWRQA PGQGLQWVGW INPKTGQPNN PRQFQGRVSL TRHASWDFDT YSFYMDLKA LRSDDTAVYF CARQRSDYWD FDVWGSGTQV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSC

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Macromolecule #2: 3BNC117 Fab light chain

MacromoleculeName: 3BNC117 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / 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 #3: PGT122 Fab heavy chain

MacromoleculeName: PGT122 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.434691 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVHLQESGPG LVKPSETLSL TCNVSGTLVR DNYWSWIRQP LGKQPEWIGY VHDSGDTNYN PSLKSRVHLS LDKSKNLVSL RLTGVTAAD SAIYYCATTK HGRRIYGVVA FKEWFTYFYM DVWGKGTSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QVHLQESGPG LVKPSETLSL TCNVSGTLVR DNYWSWIRQP LGKQPEWIGY VHDSGDTNYN PSLKSRVHLS LDKSKNLVSL RLTGVTAAD SAIYYCATTK HGRRIYGVVA FKEWFTYFYM DVWGKGTSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSC

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Macromolecule #4: PGT122 Fab light chain

MacromoleculeName: PGT122 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.712082 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TFVSVAPGQT ARITCGEESL GSRSVIWYQQ RPGQAPSLII YNNNDRPSGI PDRFSGSPGS TFGTTATLTI TSVEAGDEAD YYCHIWDSR RPTNWVFGEG TTLIVLSQPK AAPSVTLFPP SSEELQANKA TLVCLISDFY PGAVTVAWKA DSSPVKAGVE T TTPSKQSN ...String:
TFVSVAPGQT ARITCGEESL GSRSVIWYQQ RPGQAPSLII YNNNDRPSGI PDRFSGSPGS TFGTTATLTI TSVEAGDEAD YYCHIWDSR RPTNWVFGEG TTLIVLSQPK AAPSVTLFPP SSEELQANKA TLVCLISDFY PGAVTVAWKA DSSPVKAGVE T TTPSKQSN NKYAASSYLS LTPEQWKSHK SYSCQVTHEG STVEKTVAPT ECS

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Macromolecule #5: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120

MacromoleculeName: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 57.945977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK VYSLFYRLDV VQINENQGNR SNNSNKEYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCKDKKF NG TGPCPSV STVQCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QAF YATGDI IGDIRQAHCN VSKATWNETL GKVVKQLRKH FGNNTIIRFA NSSGGDLEVT THSFNCGGEF FYCNTSGLFN STWI SNTSV QGSNSTGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRD NWRS ELYKYKVVKI EPLGVAPTRC KRRVVGRRRR RR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #6: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 18.79815 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALDGSGSGG S GHHHHHHH H

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 30 / 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

Concentration0.6 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio from cryoSPARC
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 181660
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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