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- EMDB-21258: AMC009 SOSIP.v4.2 in complex with PGV04 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-21258
TitleAMC009 SOSIP.v4.2 in complex with PGV04 Fab
Map dataAMC009 SOSIP.v4.1 in complex with PGV04 Fab
Sample
  • Complex: AMC009 SOSIP.v4.2 in complex with PGV04 Fab
    • Complex: AMC009 SOSIP.v4.2
      • Protein or peptide: PGV04 heavy chain
      • Protein or peptide: PGV04 light chain
    • Complex: PGV04 Fab
      • Protein or peptide: AMC009 SOSIP.v4.2 envelope glycoprotein gp120
      • Protein or peptide: AMC009 SOSIP.v4.2 envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsCottrell CA / de Val N / Ward AB
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F31 Al131873 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: J Virol / Year: 2020
Title: Neutralizing Antibody Responses Induced by HIV-1 Envelope Glycoprotein SOSIP Trimers Derived from Elite Neutralizers.
Authors: Anna Schorcht / Tom L G M van den Kerkhof / Christopher A Cottrell / Joel D Allen / Jonathan L Torres / Anna-Janina Behrens / Edith E Schermer / Judith A Burger / Steven W de Taeye / Alba ...Authors: Anna Schorcht / Tom L G M van den Kerkhof / Christopher A Cottrell / Joel D Allen / Jonathan L Torres / Anna-Janina Behrens / Edith E Schermer / Judith A Burger / Steven W de Taeye / Alba Torrents de la Peña / Ilja Bontjer / Stephanie Gumbs / Gabriel Ozorowski / Celia C LaBranche / Natalia de Val / Anila Yasmeen / Per Johan Klasse / David C Montefiori / John P Moore / Hanneke Schuitemaker / Max Crispin / Marit J van Gils / Andrew B Ward / Rogier W Sanders /
Abstract: The induction of broadly neutralizing antibodies (bNAbs) is a major goal in vaccine research. HIV-1-infected individuals that develop exceptionally strong bNAb responses, termed elite neutralizers, ...The induction of broadly neutralizing antibodies (bNAbs) is a major goal in vaccine research. HIV-1-infected individuals that develop exceptionally strong bNAb responses, termed elite neutralizers, can inform vaccine design by providing blueprints for the induction of similar bNAb responses. We describe a new recombinant native-like envelope glycoprotein (Env) SOSIP trimer, termed AMC009, based on the viral founder sequences of an elite neutralizer. The subtype B AMC009 SOSIP protein formed stable native-like trimers that displayed multiple bNAb epitopes. Overall, its structure at 4.3-Å resolution was similar to that of BG505 SOSIP.664. The AMC009 trimer resembled one from a second elite neutralizer, AMC011, in having a dense and complete glycan shield. When tested as immunogens in rabbits, the AMC009 trimers did not induce autologous neutralizing antibody (NAb) responses efficiently while the AMC011 trimers did so very weakly, outcomes that may reflect the completeness of their glycan shields. The AMC011 trimer induced antibodies that occasionally cross-neutralized heterologous tier 2 viruses, sometimes at high titer. Cross-neutralizing antibodies were more frequently elicited by a trivalent combination of AMC008, AMC009, and AMC011 trimers, all derived from subtype B viruses. Each of these three individual trimers could deplete the NAb activity from the rabbit sera. Mapping the polyclonal sera by electron microscopy revealed that antibodies of multiple specificities could bind to sites on both autologous and heterologous trimers. These results advance our understanding of how to use Env trimers in multivalent vaccination regimens and the immunogenicity of trimers derived from elite neutralizers. Elite neutralizers, i.e., individuals who developed unusually broad and potent neutralizing antibody responses, might serve as blueprints for HIV-1 vaccine design. Here, we studied the immunogenicity of native-like recombinant envelope glycoprotein (Env) trimers based on viral sequences from elite neutralizers. While immunization with single trimers from elite neutralization did not recapitulate the breadth and potency of neutralization observed in these infected individuals, a combination of three subtype B Env trimers from elite neutralizers resulted in some neutralization breadth within subtype B viruses. These results should guide future efforts to design vaccines to induce broadly neutralizing antibodies.
History
DepositionJan 29, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.33
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.33
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vo3
  • Surface level: 0.33
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vo3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21258.png

Downloads & links

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Map

FileDownload / File: emd_21258.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAMC009 SOSIP.v4.1 in complex with PGV04 Fab
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.33 / Movie #1: 0.33
Minimum - Maximum-0.7784409 - 1.3606203
Average (Standard dev.)0.002235572 (±0.0490072)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z335.360335.360335.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ428428428
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.7781.3610.002

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Supplemental data

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Sample components

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Entire : AMC009 SOSIP.v4.2 in complex with PGV04 Fab

EntireName: AMC009 SOSIP.v4.2 in complex with PGV04 Fab
Components
  • Complex: AMC009 SOSIP.v4.2 in complex with PGV04 Fab
    • Complex: AMC009 SOSIP.v4.2
      • Protein or peptide: PGV04 heavy chain
      • Protein or peptide: PGV04 light chain
    • Complex: PGV04 Fab
      • Protein or peptide: AMC009 SOSIP.v4.2 envelope glycoprotein gp120
      • Protein or peptide: AMC009 SOSIP.v4.2 envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: AMC009 SOSIP.v4.2 in complex with PGV04 Fab

SupramoleculeName: AMC009 SOSIP.v4.2 in complex with PGV04 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: AMC009 SOSIP.v4.2

SupramoleculeName: AMC009 SOSIP.v4.2 / type: complex / 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: PGV04 Fab

SupramoleculeName: PGV04 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: PGV04 heavy chain

MacromoleculeName: PGV04 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.644771 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGSG VKKPGASVRV SCWTSEDIFE RTELIHWVRQ APGQGLEWIG WVKTVTGAVN FGSPDFRQRV SLTRDRDLFT AHMDIRGLT QGDTATYFCA RQKFYTGGQG WYFDLWGRGT LIVVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
QVQLVQSGSG VKKPGASVRV SCWTSEDIFE RTELIHWVRQ APGQGLEWIG WVKTVTGAVN FGSPDFRQRV SLTRDRDLFT AHMDIRGLT QGDTATYFCA RQKFYTGGQG WYFDLWGRGT LIVVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC

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Macromolecule #2: PGV04 light chain

MacromoleculeName: PGV04 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.073822 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGETAS LSCTAASYGH MTWYQKKPGQ PPKLLIFATS KRASGIPDRF SGSQFGKQYT LTITRMEPED FARYYCQQL EFFGQGTRLE IRRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ SGNSQESVTE Q DSKDSTYS ...String:
EIVLTQSPGT LSLSPGETAS LSCTAASYGH MTWYQKKPGQ PPKLLIFATS KRASGIPDRF SGSQFGKQYT LTITRMEPED FARYYCQQL EFFGQGTRLE IRRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ SGNSQESVTE Q DSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC

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Macromolecule #3: AMC009 SOSIP.v4.2 envelope glycoprotein gp120

MacromoleculeName: AMC009 SOSIP.v4.2 envelope glycoprotein gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.113422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ARADKLWVTV YYGVPVWKEA TTTLFCASDA KAYDTEVRNV WATHACVPTD PNPQEVVLEN VTENFNMWKN DMVEQMHEDI ISLWDQSLK PCVKLTPLCV TLNCTDYVGN ATNASTTNAT GGIGGTVERG EIKNCSFNIT TSIRDKVQKE YALFYKLDIV P IDNDNTNN ...String:
ARADKLWVTV YYGVPVWKEA TTTLFCASDA KAYDTEVRNV WATHACVPTD 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 #4: AMC009 SOSIP.v4.2 envelope glycoprotein gp41

MacromoleculeName: AMC009 SOSIP.v4.2 envelope glycoprotein gp41 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.391799 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGAIGAVFL GFLGAAGSTM GAASMTLTVQ ARQLLSGIVQ QQNNLLRAPE AQQHMLKLTV WGIKQLQARV LAVERYLRDQ QLLGIWGCS GKLICCTAVP WNNSWSNRSL DMIWNNMTWI EWEREIDNYT GLIYNLLEES QNQQEKNEQE LLELD

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 18 / 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
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 3021 / Average exposure time: 7.0 sec. / Average electron dose: 32.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 128752
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6vo3:
AMC009 SOSIP.v4.2 in complex with PGV04 Fab

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