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- EMDB-14783: AMC009 SOSIPv5.2 in complex with Fabs ACS114 and ACS122 -

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Basic information

Entry
Database: EMDB / ID: EMD-14783
TitleAMC009 SOSIPv5.2 in complex with Fabs ACS114 and ACS122
Map dataAMC009 SOSIPv5.2 ACS114 Fab ACS122 Fab
Sample
  • Complex: AMC009 SOSIPv5.2 in complex with Fabs ACS114 and ACS122
    • Protein or peptide: AMC009 SOSIPv5.2 envelope glycoprotein gp120
    • Protein or peptide: AMC009 SOSIPv5.2 envelope glycoprotein gp41
    • Protein or peptide: ACS114 heavy chain
    • Protein or peptide: ACS114 light chain
    • Protein or peptide: ACS122 heavy chain
    • Protein or peptide: ACS122 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / antibodies / silent face / gp120-gp41 interface / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.99 Å
Authorsvan Schooten J / Ozorowski G / Ward A
Funding support United States, 3 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1115782 United States
Bill & Melinda Gates FoundationINV-002916 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110657 United States
CitationJournal: PLoS Pathog / Year: 2022
Title: Complementary antibody lineages achieve neutralization breadth in an HIV-1 infected elite neutralizer.
Authors: Jelle van Schooten / Anna Schorcht / Elinaz Farokhi / Jeffrey C Umotoy / Hongmei Gao / Tom L G M van den Kerkhof / Jessica Dorning / Tim G Rijkhold Meesters / Patricia van der Woude / Judith ...Authors: Jelle van Schooten / Anna Schorcht / Elinaz Farokhi / Jeffrey C Umotoy / Hongmei Gao / Tom L G M van den Kerkhof / Jessica Dorning / Tim G Rijkhold Meesters / Patricia van der Woude / Judith A Burger / Tom Bijl / Riham Ghalaiyini / Alba Torrents de la Peña / Hannah L Turner / Celia C Labranche / Robyn L Stanfield / Devin Sok / Hanneke Schuitemaker / David C Montefiori / Dennis R Burton / Gabriel Ozorowski / Michael S Seaman / Ian A Wilson / Rogier W Sanders / Andrew B Ward / Marit J van Gils /
Abstract: Broadly neutralizing antibodies (bNAbs) have remarkable breadth and potency against most HIV-1 subtypes and are able to prevent HIV-1 infection in animal models. However, bNAbs are extremely ...Broadly neutralizing antibodies (bNAbs) have remarkable breadth and potency against most HIV-1 subtypes and are able to prevent HIV-1 infection in animal models. However, bNAbs are extremely difficult to induce by vaccination. Defining the developmental pathways towards neutralization breadth can assist in the design of strategies to elicit protective bNAb responses by vaccination. Here, HIV-1 envelope glycoproteins (Env)-specific IgG+ B cells were isolated at various time points post infection from an HIV-1 infected elite neutralizer to obtain monoclonal antibodies (mAbs). Multiple antibody lineages were isolated targeting distinct epitopes on Env, including the gp120-gp41 interface, CD4-binding site, silent face and V3 region. The mAbs each neutralized a diverse set of HIV-1 strains from different clades indicating that the patient's remarkable serum breadth and potency might have been the result of a polyclonal mixture rather than a single bNAb lineage. High-resolution cryo-electron microscopy structures of the neutralizing mAbs (NAbs) in complex with an Env trimer generated from the same individual revealed that the NAbs used multiple strategies to neutralize the virus; blocking the receptor binding site, binding to HIV-1 Env N-linked glycans, and disassembly of the trimer. These results show that diverse NAbs can complement each other to achieve a broad and potent neutralizing serum response in HIV-1 infected individuals. Hence, the induction of combinations of moderately broad NAbs might be a viable vaccine strategy to protect against a wide range of circulating HIV-1 viruses.
History
DepositionApr 15, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14783.png

Downloads & links

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Map

FileDownload / File: emd_14783.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAMC009 SOSIPv5.2 ACS114 Fab ACS122 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 300 pix.
= 345. Å		1.15 Å/pix.
x 300 pix.
= 345. Å		1.15 Å/pix.
x 300 pix.
= 345. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.7314662 - 1.1641225
Average (Standard dev.)0.00068869145 (±0.031770587)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 345.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14783_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AMC009 SOSIPv5.2 ACS114 Fab ACS122 Fab half map A

Fileemd_14783_half_map_1.map
AnnotationAMC009 SOSIPv5.2 ACS114 Fab ACS122 Fab half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AMC009 SOSIPv5.2 ACS114 Fab ACS122 Fab half map B

Fileemd_14783_half_map_2.map
AnnotationAMC009 SOSIPv5.2 ACS114 Fab ACS122 Fab half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AMC009 SOSIPv5.2 in complex with Fabs ACS114 and ACS122

EntireName: AMC009 SOSIPv5.2 in complex with Fabs ACS114 and ACS122
Components
  • Complex: AMC009 SOSIPv5.2 in complex with Fabs ACS114 and ACS122
    • Protein or peptide: AMC009 SOSIPv5.2 envelope glycoprotein gp120
    • Protein or peptide: AMC009 SOSIPv5.2 envelope glycoprotein gp41
    • Protein or peptide: ACS114 heavy chain
    • Protein or peptide: ACS114 light chain
    • Protein or peptide: ACS122 heavy chain
    • Protein or peptide: ACS122 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: AMC009 SOSIPv5.2 in complex with Fabs ACS114 and ACS122

SupramoleculeName: AMC009 SOSIPv5.2 in complex with Fabs ACS114 and ACS122
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17 kDa/nm

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Macromolecule #1: AMC009 SOSIPv5.2 envelope glycoprotein gp120

MacromoleculeName: AMC009 SOSIPv5.2 envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.145488 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ARADKLWVTV YYGVPVWKEA TTTLFCASDA KAYDTEVRNV WATHCCVPTD PNPQEVVLEN VTENFNMWKN DMVEQMHEDI ISLWDQSLK PCVKLTPLCV TLNCTDYVGN ATNASTTNAT GGIGGTVERG EIKNCSFNIT TSIRDKVQKE YALFYKLDIV P IDNDNTNN ...String:
ARADKLWVTV YYGVPVWKEA TTTLFCASDA KAYDTEVRNV WATHCCVPTD PNPQEVVLEN VTENFNMWKN DMVEQMHEDI ISLWDQSLK PCVKLTPLCV TLNCTDYVGN ATNASTTNAT GGIGGTVERG EIKNCSFNIT TSIRDKVQKE YALFYKLDIV P IDNDNTNN SYRLINCNTS VIKQACPKVS FEPIPIHYCA PAGFAILKCN DKKFNGTGPC TNVSTVQCTH GIRPVVSTQL LL NGSLAEK EVVIRSQNFT NNAKVIIVQL NESVVINCTR PNNNTRKSIH IAPGRWFYTT GAIIGDIRQA HCNISRVKWN NTL KQIATK LREQFKNKTI AFNQSSGGDP EIVMHSFNCG GEFFYCNTTQ LFNSTWNDTE VSNYNDITHI TLPCRIKQII NMWQ KVGKA MYAPPIRGQI RCSSNITGLL LTRDGGSNEN KTSETETFRP AGGDMRDNWR SELYKYKVVK IEPLGVAPTK CKRRV VQ

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Macromolecule #2: AMC009 SOSIPv5.2 envelope glycoprotein gp41

MacromoleculeName: AMC009 SOSIPv5.2 envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.423865 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGAIGAVFL GFLGAAGSTM GAASMTLTVQ ARQLLSGIVQ QQNNLLRAPE CQQHMLKLTV WGIKQLQARV LAVERYLRDQ QLLGIWGCS GKLICCTAVP WNNSWSNRSL DMIWNNMTWI EWEREIDNYT GLIYNLLEES QNQQEKNEQE LLELD

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Macromolecule #3: ACS114 heavy chain

MacromoleculeName: ACS114 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.280985 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQQWGGG LLKPSQTLSL TCAVYRWTFN DHYWSWVRQS PGKGLEWIGE ISWGGATNYN PSLKSRVTMS VDTSMSHVSL KMTSVTAAD TGVYYCVRVG PGPHMAALDY WGHGSRVLVS S

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Macromolecule #4: ACS114 light chain

MacromoleculeName: ACS114 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.186664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQTPLS SPVTLGQPAS ISCGSSQSLV HSDGNTYLSW LQQRPGQPPR LLIYKISNRI SGLPDRFSGS GAETNFTLKI SRVEAEDVG LYYCVQGTQF PWTSGQGTKV EIK

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Macromolecule #5: ACS122 heavy chain

MacromoleculeName: ACS122 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.774439 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSEALSL TCSVSGVAIS RHYWNWIRQP PGKGLEWIGY IFFNGNTNYS PSLKSRVTIS VDTSKNEFSL TLRSVTAAD TAVYYCAREK SVVEPDNMVR WFDPWGQGTL VTVSS

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Macromolecule #6: ACS122 light chain

MacromoleculeName: ACS122 light chain / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.668917 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYELTQPPSV SVAPGKTARI TCGGNNIGSK SVHWYQQKPG QAPVLVIYYD SDRPSGIPER FSGSKSGNTA TLTISRVEAG DEADYYCQV WDSSRDHCVF GIGTKVTVL

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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: 21 / 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: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 49.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vo3

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 159597
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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