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- EMDB-13316: HIV-1 Env (BG505 SOSIP.664) in complex with the IgA bNAb 7-269 an... -

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Entry
Database: EMDB / ID: EMD-13316
TitleHIV-1 Env (BG505 SOSIP.664) in complex with the IgA bNAb 7-269 and the antibody 3BNC117.
Map dataMap corresponding to the Env 7269 3BNC117 complex
Sample
  • Complex: Ternary complex of HIV Env (BG505 SOSIP.664) with bNAbs 3BNC117 (IgG Fab) and 7269 (IgA Fab)
    • Complex: Env protomer with one 3BNC117 Fab and one 7-269 Fab
      • Protein or peptide: 7-269 IgA Fab heavy chain
      • Protein or peptide: 7-269 IgA Fab light chain
      • Protein or peptide: gp120, BG505 SOSIP.664 T332N
      • Protein or peptide: gp41 BG505 T332N SOSIP.664
      • Protein or peptide: 3BNC IgG Fab heavy chain
      • Protein or peptide: 3BNC117 IgG Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV / antibody / bNAb / Env / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Human immunodeficiency virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsFernandez I / Bontems F
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Exp Med / Year: 2022
Title: Epitope convergence of broadly HIV-1 neutralizing IgA and IgG antibody lineages in a viremic controller.
Authors: Valérie Lorin / Ignacio Fernández / Guillemette Masse-Ranson / Mélanie Bouvin-Pley / Luis M Molinos-Albert / Cyril Planchais / Thierry Hieu / Gérard Péhau-Arnaudet / Dominik Hrebík / ...Authors: Valérie Lorin / Ignacio Fernández / Guillemette Masse-Ranson / Mélanie Bouvin-Pley / Luis M Molinos-Albert / Cyril Planchais / Thierry Hieu / Gérard Péhau-Arnaudet / Dominik Hrebík / Giulia Girelli-Zubani / Oriane Fiquet / Florence Guivel-Benhassine / Rogier W Sanders / Bruce D Walker / Olivier Schwartz / Johannes F Scheid / Jordan D Dimitrov / Pavel Plevka / Martine Braibant / Michael S Seaman / François Bontems / James P Di Santo / Félix A Rey / Hugo Mouquet /
Abstract: Decrypting the B cell ontogeny of HIV-1 broadly neutralizing antibodies (bNAbs) is paramount for vaccine design. Here, we characterized IgA and IgG bNAbs of three distinct B cell lineages in a ...Decrypting the B cell ontogeny of HIV-1 broadly neutralizing antibodies (bNAbs) is paramount for vaccine design. Here, we characterized IgA and IgG bNAbs of three distinct B cell lineages in a viremic controller, two of which comprised only IgG+ or IgA+ blood memory B cells; the third combined both IgG and IgA clonal variants. 7-269 bNAb in the IgA-only lineage displayed the highest neutralizing capacity despite limited somatic mutation, and delayed viral rebound in humanized mice. bNAbs in all three lineages targeted the N332 glycan supersite. The 2.8-Å resolution cryo-EM structure of 7-269-BG505 SOSIP.664 complex showed a similar pose as 2G12, on an epitope mainly composed of sugar residues comprising the N332 and N295 glycans. Binding and cryo-EM structural analyses showed that antibodies from the two other lineages interact mostly with glycans N332 and N386. Hence, multiple B cell lineages of IgG and IgA bNAbs focused on a unique HIV-1 site of vulnerability can codevelop in HIV-1 viremic controllers.
History
DepositionAug 3, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.29
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.29
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pc2
  • Surface level: 0.29
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13316.png

Downloads & links

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Map

FileDownload / File: emd_13316.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap corresponding to the Env 7269 3BNC117 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 420 pix.
= 357. Å		0.85 Å/pix.
x 420 pix.
= 357. Å		0.85 Å/pix.
x 420 pix.
= 357. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29 / Movie #1: 0.29
Minimum - Maximum-0.6588376 - 2.634463
Average (Standard dev.)0.0011493887 (±0.049394008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 357.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z357.000357.000357.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.6592.6340.001

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Supplemental data

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Mask #1

Fileemd_13316_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map obtained by local refinement applying a mask on one protomer

Fileemd_13316_additional_1.map
AnnotationMap obtained by local refinement applying a mask on one protomer
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 HIV Env (BG505 SOSIP.664) with bNAbs 3BNC117 (...

EntireName: Ternary complex of HIV Env (BG505 SOSIP.664) with bNAbs 3BNC117 (IgG Fab) and 7269 (IgA Fab)
Components
  • Complex: Ternary complex of HIV Env (BG505 SOSIP.664) with bNAbs 3BNC117 (IgG Fab) and 7269 (IgA Fab)
    • Complex: Env protomer with one 3BNC117 Fab and one 7-269 Fab
      • Protein or peptide: 7-269 IgA Fab heavy chain
      • Protein or peptide: 7-269 IgA Fab light chain
      • Protein or peptide: gp120, BG505 SOSIP.664 T332N
      • Protein or peptide: gp41 BG505 T332N SOSIP.664
      • Protein or peptide: 3BNC IgG Fab heavy chain
      • Protein or peptide: 3BNC117 IgG Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of HIV Env (BG505 SOSIP.664) with bNAbs 3BNC117 (...

SupramoleculeName: Ternary complex of HIV Env (BG505 SOSIP.664) with bNAbs 3BNC117 (IgG Fab) and 7269 (IgA Fab)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Env protomer with one 3BNC117 Fab and one 7-269 Fab

SupramoleculeName: Env protomer with one 3BNC117 Fab and one 7-269 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 7-269 IgA Fab heavy chain

MacromoleculeName: 7-269 IgA Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.425404 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QMQLVESGGG VVQPGRSLRL SCAASRFDFN RFGMHWVRQA PGKGLEWVAY MSYDGGDRYY ADSVKGRFTI SRDNSKSTLH LQMDSLRPE DTAVYYCAKD DILGDCSTSH CYWGYYYQGM DVWGHGTTVT VSSASTTSPK VFPLSLCSTQ PDGNVVIACL V QGFFPQEP ...String:
QMQLVESGGG VVQPGRSLRL SCAASRFDFN RFGMHWVRQA PGKGLEWVAY MSYDGGDRYY ADSVKGRFTI SRDNSKSTLH LQMDSLRPE DTAVYYCAKD DILGDCSTSH CYWGYYYQGM DVWGHGTTVT VSSASTTSPK VFPLSLCSTQ PDGNVVIACL V QGFFPQEP LSVTWSESGQ GVTARNFPPS QDASGDLYTT SSQLTLPATQ CLAGKSVTCH VKHYTNPSQD VTVPCPHHHH HH

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Macromolecule #2: 7-269 IgA Fab light chain

MacromoleculeName: 7-269 IgA Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.520053 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVMTQSPDT LSVSPGERVT LSCRASQSVG SNLVWYQQKP GQSTRVLIYG ASTRAATVPA RFSGGGSGTE FTLTISSVQS EDFAVYYCY HYNNWPRGSF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVMTQSPDT LSVSPGERVT LSCRASQSVG SNLVWYQQKP GQSTRVLIYG ASTRAATVPA RFSGGGSGTE FTLTISSVQS EDFAVYYCY HYNNWPRGSF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #3: gp120, BG505 SOSIP.664 T332N

MacromoleculeName: gp120, BG505 SOSIP.664 T332N / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus / Strain: BG505
Molecular weightTheoretical: 54.064277 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ AMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R

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Macromolecule #4: gp41 BG505 T332N SOSIP.664

MacromoleculeName: gp41 BG505 T332N SOSIP.664 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus / Strain: BG505
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #5: 3BNC IgG Fab heavy chain

MacromoleculeName: 3BNC IgG Fab heavy chain / type: protein_or_peptide / ID: 5 / 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 #6: 3BNC117 IgG Fab light chain

MacromoleculeName: 3BNC117 IgG Fab light chain / type: protein_or_peptide / ID: 6 / 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 #15: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 15 / Number of copies: 20 / 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

Concentration0.3 mg/mL
BufferpH: 8 / Component:
ConcentrationName
10.0 mMTris
75.0 mMNaCl
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 287 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115394
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: RELION (ver. 3.1)

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Atomic model buiding 1

Initial modelPDB ID:

5v8m


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7pc2:
HIV-1 Env (BG505 SOSIP.664) in complex with the IgA bNAb 7-269 and the antibody 3BNC117.

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