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- EMDB-43967: HIV 16055.v8.3 SOSIP Env in Complex with Base and N625 Epitope pA... -

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Basic information

Entry
Database: EMDB / ID: EMD-43967
TitleHIV 16055.v8.3 SOSIP Env in Complex with Base and N625 Epitope pAbs from Rabbit 2463
Map data
Sample
  • Complex: HIV 16055 SOSIP Env in Complex with Base and N625 Epitope Polyclonal Antibodies
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: Rabbit Polyclonal Antibody N625 Epitope - Predicted Light Chain
    • Protein or peptide: Rabbit Polyclonal Antibody N625 Epitope - Predicted Heavy Chain
    • Protein or peptide: Rabbit Polyclonal Antibody Base Epitope - Predicted Heavy Chain
    • Protein or peptide: Rabbit Polyclonal Antibody Base Epitope - Predicted Light Chain
    • Protein or peptide: Surface protein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose
KeywordsHIV / EMPEM / Polyclonal Antibodies / Rabbit / N625 / Base / SOSIP / 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBrown S / Antanasijevic A / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136621 United States
Bill & Melinda Gates FoundationUM1 AI100663 United States
CitationJournal: Sci Immunol / Year: 2025
Title: Anti-immune complex antibodies are elicited during repeated immunization with HIV Env immunogens.
Authors: Sharidan Brown / Aleksandar Antanasijevic / Leigh M Sewall / Daniel Montiel Garcia / James Ferguson / Philip J M Brouwer / Rogier W Sanders / Andrew B Ward /
Abstract: Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody ...Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody responses are directed to easily accessible nonneutralizing epitopes on Env instead of bnAb epitopes. Autologously neutralizing antibody responses appear upon boosting, once immunodominant epitopes are saturated. Here, we use electron microscopy-based polyclonal epitope mapping (EMPEM) to elucidate how repeated immunization with HIV Env SOSIP immunogens results in the generation of Ab2α anti-idiotypic antibodies in rabbits and rhesus macaques. We present the structures of six anti-immune complex antibodies and find that they target idiotopes composed of framework regions of antibodies bound to Env. Examination of cryo-electron microscopy density enabled prediction of sequences for an anti-immune complex antibody, the paratope of which is enriched with aromatic amino acids. This work sheds light on current vaccine development efforts for HIV, as well as for other pathogens in which repeated exposure to antigen is required.
History
DepositionMar 6, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43967.png

Downloads & links

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Map

FileDownload / File: emd_43967.map.gz / Format: CCP4 / Size: 421.9 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.)
0.8 Å/pix.
x 480 pix.
= 384.72 Å		0.8 Å/pix.
x 480 pix.
= 384.72 Å		0.8 Å/pix.
x 480 pix.
= 384.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8015 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.04410524 - 0.07769011
Average (Standard dev.)0.000036273403 (±0.0021181307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 384.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43967_msk_1.map
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Half map: #1

Fileemd_43967_half_map_1.map
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Half map: #2

Fileemd_43967_half_map_2.map
Projections & Slices
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Sample components

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Entire : HIV 16055 SOSIP Env in Complex with Base and N625 Epitope Polyclo...

EntireName: HIV 16055 SOSIP Env in Complex with Base and N625 Epitope Polyclonal Antibodies
Components
  • Complex: HIV 16055 SOSIP Env in Complex with Base and N625 Epitope Polyclonal Antibodies
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: Rabbit Polyclonal Antibody N625 Epitope - Predicted Light Chain
    • Protein or peptide: Rabbit Polyclonal Antibody N625 Epitope - Predicted Heavy Chain
    • Protein or peptide: Rabbit Polyclonal Antibody Base Epitope - Predicted Heavy Chain
    • Protein or peptide: Rabbit Polyclonal Antibody Base Epitope - Predicted Light Chain
    • Protein or peptide: Surface protein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: HIV 16055 SOSIP Env in Complex with Base and N625 Epitope Polyclo...

SupramoleculeName: HIV 16055 SOSIP Env in Complex with Base and N625 Epitope Polyclonal Antibodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Transmembrane protein gp41

MacromoleculeName: Transmembrane protein gp41 / type: protein_or_peptide / ID: 1 / Details: The sequence contains engineered SOSIP mutations. / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.430652 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RRAVGLGAVS FGFLGAAGST MGAASITLTV QARQLLSGIV QQQSNLLKAP ECQQHLLQDG HWGIKQLQTR VLAIEHYLKD QQLLGIWGC SGKLICCTAV PWNSSWSNKS HDEIWGNMTW MQWDREISNY TNTIYRLLED SQNQQEQNEK DLLALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Rabbit Polyclonal Antibody N625 Epitope - Predicted Light Chain

MacromoleculeName: Rabbit Polyclonal Antibody N625 Epitope - Predicted Light Chain
type: protein_or_peptide / ID: 2
Details: The sequence of the polyclonal antibody is unknown and modeled as a poly-UNK chain.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 9.379553 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: Rabbit Polyclonal Antibody N625 Epitope - Predicted Heavy Chain

MacromoleculeName: Rabbit Polyclonal Antibody N625 Epitope - Predicted Heavy Chain
type: protein_or_peptide / ID: 3
Details: The sequence of the polyclonal antibody is unknown and modeled as a poly-UNK chain.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 10.145497 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #4: Rabbit Polyclonal Antibody Base Epitope - Predicted Heavy Chain

MacromoleculeName: Rabbit Polyclonal Antibody Base Epitope - Predicted Heavy Chain
type: protein_or_peptide / ID: 4
Details: The sequence of the polyclonal antibody is unknown and modeled as a poly-UNK chain.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 10.400812 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #5: Rabbit Polyclonal Antibody Base Epitope - Predicted Light Chain

MacromoleculeName: Rabbit Polyclonal Antibody Base Epitope - Predicted Light Chain
type: protein_or_peptide / ID: 5
Details: The sequence of the polyclonal antibody is unknown and modeled as a poly-UNK chain.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 9.294448 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #6: Surface protein gp120

MacromoleculeName: Surface protein gp120 / type: protein_or_peptide / ID: 6
Details: The sequence contains engineered SOSIP mutations. The sequence contains an expression tag and initiating methionine residue.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 58.156312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARNGNLW VTVYYGVPVW KDAETTLFCA SDAKAYEKEK RNVWATHCCV PTDPNPQEM VLENVTENFN MWKNDMVEQM HEDVISLWDQ SLKPCVKLTP LCVTLECRQV NTTNATSSVN VTNGEEIKNC S FNATTELR ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARNGNLW VTVYYGVPVW KDAETTLFCA SDAKAYEKEK RNVWATHCCV PTDPNPQEM VLENVTENFN MWKNDMVEQM HEDVISLWDQ SLKPCVKLTP LCVTLECRQV NTTNATSSVN VTNGEEIKNC S FNATTELR DKKQKVYALF YRLDIVPLEE ERKGNSSKYR LINCNTSAIT QACPKVTFDP IPIHYCAPAG YAILKCNNKT FN GTGPCNN VSTVQCTHGI KPVVSTQLLL NGSLAEGEII IRSENLTNNV KTIIVHLNES VEIVCTRPNN NTVKSIRIGP GQW FYYTGD IIGNIRQAYC NIKKDDWIRT LQRVGKKLAE HFPRRIINFT QPAGGDLEIT THSFNCRGEF FYCNTSSLFN STYN PNDTN SNSSSSNSSL DITIPCRIKQ IINMWQRVGQ AMYAPPIEGN ITCKSNITGL LLVRDGGVES NETEIFRPGG GDMRN NWRS ELYKYKVVEI KPLGIAPTRC KRRVVERRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 33 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #12: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 12 / Number of copies: 1 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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

Concentration4.2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3798 / Average electron dose: 40.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Initial model generated from a low pass filtered map of BG505 SOSIP.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 51733
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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