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- EMDB-24675: AMC018 SOSIP.v4.2 in complex with PGV04 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-24675
TitleAMC018 SOSIP.v4.2 in complex with PGV04 Fab
Map dataAMC018 SOSIP.v4.2 in complex with PGV04 Fab
Sample
  • Complex: AMC018 SOSIP.v4.2 in complex with PGV04 Fab
    • Protein or peptide: AMC018 gp120
    • Protein or peptide: AMC018 gp41
    • Protein or peptide: PGV04 Fab heavy chain
    • Protein or peptide: PGV04 kappa chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsCottrell CA / de Val N / Ward AB
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 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)F31 AI131873 United States
CitationJournal: J Virol / Year: 2022
Title: The Glycan Hole Area of HIV-1 Envelope Trimers Contributes Prominently to the Induction of Autologous Neutralization.
Authors: Anna Schorcht / Christopher A Cottrell / Pavel Pugach / Rajesh P Ringe / Alvin X Han / Joel D Allen / Tom L G M van den Kerkhof / Gemma E Seabright / Edith E Schermer / Thomas J Ketas / ...Authors: Anna Schorcht / Christopher A Cottrell / Pavel Pugach / Rajesh P Ringe / Alvin X Han / Joel D Allen / Tom L G M van den Kerkhof / Gemma E Seabright / Edith E Schermer / Thomas J Ketas / Judith A Burger / Jelle van Schooten / Celia C LaBranche / Gabriel Ozorowski / Natalia de Val / Daniel L V Bader / Hanneke Schuitemaker / Colin A Russell / David C Montefiori / Marit J van Gils / Max Crispin / P J Klasse / Andrew B Ward / John P Moore / Rogier W Sanders /
Abstract: The human immunodeficiency virus type 1 (HIV-1) trimeric envelope glycoprotein (Env) is heavily glycosylated, creating a dense glycan shield that protects the underlying peptidic surface from ...The human immunodeficiency virus type 1 (HIV-1) trimeric envelope glycoprotein (Env) is heavily glycosylated, creating a dense glycan shield that protects the underlying peptidic surface from antibody recognition. The absence of conserved glycans, due to missing potential N-linked glycosylation sites (PNGS), can result in strain-specific, autologous neutralizing antibody (NAb) responses. Here, we sought to gain a deeper understanding of the autologous neutralization by introducing holes in the otherwise dense glycan shields of the AMC011 and AMC016 SOSIP trimers. Specifically, when we knocked out the N130 and N289 glycans, which are absent from the well-characterized B41 SOSIP trimer, we observed stronger autologous NAb responses. We also analyzed the highly variable NAb responses induced in rabbits by diverse SOSIP trimers from subtypes A, B, and C. Statistical analysis, using linear regression, revealed that the cumulative area exposed on a trimer by glycan holes correlates with the magnitude of the autologous NAb response. Forty years after the first description of HIV-1, the search for a protective vaccine is still ongoing. The sole target for antibodies that can neutralize the virus are the trimeric envelope glycoproteins (Envs) located on the viral surface. The glycoprotein surface is covered with glycans that shield off the underlying protein components from recognition by the immune system. However, the Env trimers of some viral strains have holes in the glycan shield. Immunized animals developed antibodies against such glycan holes. These antibodies are generally strain specific. Here, we sought to gain a deeper understanding of what drives these specific immune responses. First, we show that strain-specific neutralizing antibody responses can be increased by creating artificial holes in the glycan shield. Second, when studying a diverse set of Env trimers with different characteristics, we found that the surface area of the glycan holes contributes prominently to the induction of strain-specific neutralizing antibodies.
History
DepositionAug 11, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateJan 26, 2022-
Current statusJan 26, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rsn
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24675.png

Downloads & links

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Map

FileDownload / File: emd_24675.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAMC018 SOSIP.v4.2 in complex with PGV04 Fab
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.55 / Movie #1: 0.55
Minimum - Maximum-2.0537417 - 3.9185011
Average (Standard dev.)0.001706517 (±0.099647425)
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/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.0543.9190.002

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Supplemental data

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Half map: AMC018 SOSIP.v4.2 in complex with PGV04 Fab

Fileemd_24675_half_map_1.map
AnnotationAMC018 SOSIP.v4.2 in complex with PGV04 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AMC018 SOSIP.v4.2 in complex with PGV04 Fab

Fileemd_24675_half_map_2.map
AnnotationAMC018 SOSIP.v4.2 in complex with PGV04 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AMC018 SOSIP.v4.2 in complex with PGV04 Fab

EntireName: AMC018 SOSIP.v4.2 in complex with PGV04 Fab
Components
  • Complex: AMC018 SOSIP.v4.2 in complex with PGV04 Fab
    • Protein or peptide: AMC018 gp120
    • Protein or peptide: AMC018 gp41
    • Protein or peptide: PGV04 Fab heavy chain
    • Protein or peptide: PGV04 kappa chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: AMC018 SOSIP.v4.2 in complex with PGV04 Fab

SupramoleculeName: AMC018 SOSIP.v4.2 in complex with PGV04 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: AMC018 gp120

MacromoleculeName: AMC018 gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.705789 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AGNLWVTVYY GVPVWKEATT TLFCASDARA YETEARNVWA THACVPTDPN PQEVVLENVT ENFNMWRNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL NCSDMGNETA TNNTSSGGET VEKGEIKNCS FNITTNIRDK VQKVYATFYK LDIVPIDDKT N NNNTNYTN ...String:
AGNLWVTVYY GVPVWKEATT TLFCASDARA YETEARNVWA THACVPTDPN PQEVVLENVT ENFNMWRNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL NCSDMGNETA TNNTSSGGET VEKGEIKNCS FNITTNIRDK VQKVYATFYK LDIVPIDDKT N NNNTNYTN YRLISCNTSV LTQACPKISF EPIPIHYCAP AGFAILKCNN KTFNGKGPCT NVSTVQCTHG IRPVVSTQLL LN GSLAEEE VVIRSENFTD NAKTIIVQLN ESVEINCTRP NNNTRRSISI GPGRWFYTTG EIIGNIRQAH CNISRAKWNN TLQ QIVNKL REKFENKTIV FNQPSGGDPE IVMHSFNCGG EFFYCNTTQL FNSTWNDTGG SNNTEGNNTI TLPCRIKQII NMWQ EVGKA MYAPPIKGQI RCSSNITGLL LTRDGGKTTN NTEIFRPGGG DMRDNWRSEL YKYKVVKIEP LGIAPTKCKR RVVQR RRRR R

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Macromolecule #2: AMC018 gp41

MacromoleculeName: AMC018 gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.152566 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMALTVQA RQLLSGIVQQ QNNLLRAPEA QQHMLKLTVW GIKQLQARVL AVERYLKDQQ LLGIWGCSG KLICCTAVPW NASWSNKSVD EIWGNMTWMQ WEREIDNYTS LIYTLIEESQ NQQEKNEQEL LELD

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Macromolecule #3: PGV04 Fab heavy chain

MacromoleculeName: PGV04 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.759861 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 D

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Macromolecule #4: PGV04 kappa chain

MacromoleculeName: PGV04 kappa chain / type: protein_or_peptide / ID: 4 / 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 #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 30 / 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: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3916 / Average exposure time: 7.0 sec. / Average electron dose: 26.6 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 150333
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7rsn:
AMC018 SOSIP.v4.2 in complex with PGV04 Fab

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