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- EMDB-14474: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124 -

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Basic information

Entry
Database: EMDB / ID: EMD-14474
TitleAMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
Map dataAMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124 (main map)
Sample
  • Complex: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
    • Complex: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
      • Protein or peptide: AMC009 SOSIPv5.2 envelope glycoprotein gp120
      • Protein or peptide: AMC009 SOSIP.v5.2 envelope glycoprotein gp41
    • Complex: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
      • Protein or peptide: ACS124 heavy chain
      • Protein or peptide: ACS124 light chain
      • Protein or peptide: ACS101 heavy chain
      • Protein or peptide: ACS101 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
Authorsvan Schooten J / 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: Nat Commun / Year: 2022
Title: Identification of IOMA-class neutralizing antibodies targeting the CD4-binding site on the HIV-1 envelope glycoprotein.
Authors: Jelle van Schooten / Elinaz Farokhi / Anna Schorcht / Tom L G M van den Kerkhof / Hongmei Gao / Patricia van der Woude / Judith A Burger / Tim G Rijkhold Meesters / Tom Bijl / Riham ...Authors: Jelle van Schooten / Elinaz Farokhi / Anna Schorcht / Tom L G M van den Kerkhof / Hongmei Gao / Patricia van der Woude / Judith A Burger / Tim G Rijkhold Meesters / Tom Bijl / Riham Ghalaiyini / Hannah L Turner / Jessica Dorning / Barbera D C van Schaik / Antoine H C van Kampen / Celia C Labranche / Robyn L Stanfield / Devin Sok / David C Montefiori / Dennis R Burton / Michael S Seaman / Gabriel Ozorowski / Ian A Wilson / Rogier W Sanders / Andrew B Ward / Marit J van Gils /
Abstract: A major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope ...A major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope glycoprotein is of interest because, unlike the better-known VH1-2-derived VRC01-class bNAbs, it does not require a rare short light chain complementarity-determining region 3 (CDRL3). Here, we describe three IOMA-class NAbs, ACS101-103, with up to 37% breadth, that share many characteristics with IOMA, including an average-length CDRL3. Cryo-electron microscopy revealed that ACS101 shares interactions with those observed with other VH1-2 and VH1-46-class bNAbs, but exhibits a unique binding mode to residues in loop D. Analysis of longitudinal sequences from the patient suggests that a transmitter/founder-virus lacking the N276 glycan might have initiated the development of these NAbs. Together these data strengthen the rationale for germline-targeting vaccination strategies to induce IOMA-class bNAbs and provide a wealth of sequence and structural information to support such strategies.
History
DepositionMar 2, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateAug 17, 2022-
Current statusAug 17, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14474.png

Downloads & links

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Map

FileDownload / File: emd_14474.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124 (main map)
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.37285718 - 0.8603995
Average (Standard dev.)0.00021460386 (±0.029345945)
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_14474_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124 (main map)

Fileemd_14474_additional_1.map
AnnotationAMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124 (main map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124 (half map A)

Fileemd_14474_additional_2.map
AnnotationAMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124 (half map A)
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 ACS101 and ACS124

EntireName: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
Components
  • Complex: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
    • Complex: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
      • Protein or peptide: AMC009 SOSIPv5.2 envelope glycoprotein gp120
      • Protein or peptide: AMC009 SOSIP.v5.2 envelope glycoprotein gp41
    • Complex: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
      • Protein or peptide: ACS124 heavy chain
      • Protein or peptide: ACS124 light chain
      • Protein or peptide: ACS101 heavy chain
      • Protein or peptide: ACS101 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124

SupramoleculeName: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Molecular weightTheoretical: 17 kDa/nm

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Supramolecule #2: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124

SupramoleculeName: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124

SupramoleculeName: AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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 SOSIP.v5.2 envelope glycoprotein gp41

MacromoleculeName: AMC009 SOSIP.v5.2 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: ACS124 heavy chain

MacromoleculeName: ACS124 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.892636 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLLESGPG LVKPSETLSL TCTVSGVPIS RHYWNWIRQS PGKGLEWIGY IFFNGNANYN PSLKSRVTIS VDMSKNQFSL TLRSVTAAD TAVYYCVREK SIAEEDNMVR WFDPWGQGTL VTVSS

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Macromolecule #4: ACS124 light chain

MacromoleculeName: ACS124 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.67387 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYELTQPPSV SVAPGKTARI TCGGNNLGTK SVHWYQQKPG QAPVNVIYYD SDRPSGIPER FSGSKSGNTA TLTISRVEAG DEADYYCQV WDSSRDQCVF GIGTKVTVL

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Macromolecule #5: ACS101 heavy chain

MacromoleculeName: ACS101 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.147723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLLESGAE VKKPGASVRV SCEASGYTFT KYFIHWVRQA PGHGLEWIGW INTLTSGVNY ARNFQGRLTL TRDLSTETVY MDLRNLKSD DTAVYYCARG GRGYDEPWGA YTWLDPWGQG SLVTVSS

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Macromolecule #6: ACS101 light chain

MacromoleculeName: ACS101 light chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.51382 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VTSYELTQPA SVSGSPGQSI TISCTGSSIG SYDLVSWYQQ YPGKAPKVII FEVSKRPSGV SHRFSGSKSG NTAALTISGL QVEDEAIYH CYSYDDMIIF GGGTRLTVL

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

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 49.0 e/Å2
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

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 95062
FSC plot (resolution estimation)

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