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- EMDB-24676: AMC016 SOSIP.v4.2 in complex with PGV04 Fab -

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Entry
Database: EMDB / ID: EMD-24676
TitleAMC016 SOSIP.v4.2 in complex with PGV04 Fab
Map dataAMC016 SOSIP.v4.2 in complex with PGV04 Fab
Sample
  • Complex: AMC016 SOSIP.v4.2 in complex with PGV04 Fab
    • Protein or peptide: AMC016 gp120
    • Protein or peptide: AMC016 gp41
    • Protein or peptide: PGV04 Fab heavy chain
    • Protein or peptide: PGV04 kappa chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV / Env / antibody / bnAb / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsBader DLV / Cottrell CA / 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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rso
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rso
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24676.png

Downloads & links

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Map

FileDownload / File: emd_24676.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAMC016 SOSIP.v4.2 in complex with PGV04 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-1.4492644 - 2.7076387
Average (Standard dev.)0.0014382759 (±0.065816134)
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-1.4492.7080.001

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Supplemental data

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Half map: AMC016 SOSIP.v4.2 in complex with PGV04 Fab

Fileemd_24676_half_map_1.map
AnnotationAMC016 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: AMC016 SOSIP.v4.2 in complex with PGV04 Fab

Fileemd_24676_half_map_2.map
AnnotationAMC016 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 : AMC016 SOSIP.v4.2 in complex with PGV04 Fab

EntireName: AMC016 SOSIP.v4.2 in complex with PGV04 Fab
Components
  • Complex: AMC016 SOSIP.v4.2 in complex with PGV04 Fab
    • Protein or peptide: AMC016 gp120
    • Protein or peptide: AMC016 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: AMC016 SOSIP.v4.2 in complex with PGV04 Fab

SupramoleculeName: AMC016 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: AMC016 gp120

MacromoleculeName: AMC016 gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.890215 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AEEELWVTVY YGVPVWKEAT TTLFCASDAK AYDTEVRNVW ATHACVPTDP SPQEVVLANV TENFNMWKNN MVEQMHEDII SLWDQSLKP CVKLTPLCVT LNCTDLGNAT DAINRNTTDA PNSTLRTMEE KGEIKNCSFN ITTSVRDKMQ KEYATFYKLD I VPIDNDNN ...String:
AEEELWVTVY YGVPVWKEAT TTLFCASDAK AYDTEVRNVW ATHACVPTDP SPQEVVLANV TENFNMWKNN MVEQMHEDII SLWDQSLKP CVKLTPLCVT LNCTDLGNAT DAINRNTTDA PNSTLRTMEE KGEIKNCSFN ITTSVRDKMQ KEYATFYKLD I VPIDNDNN SYRLINCNTS VITQACPKVS FEPIPIHYCA PAGFAILKCN NKTFNGTGPC TNVSTVQCTH GIRPVVSTQL LL NGSLAEE EIVIRSENFT DNAKTIIVQL NESVEINCTR PNNNTRKSIH IGPGRWFYTT GQIIGNIRQA HCNISRAKWN NTL HKIVKK LREQFRNKTI VFKQSSGGDP EIVMHSFNCG GEFFYCNSTQ LFNSTWYGNE SSDNPGVEGN ITLPCRIKQI INLW QEVGK AMYAPPIGGQ IRCSSNITGL LLTRDGGNNN ITTEIFRPGG GDMRDNWRSE LYKYKVVKIE PLGVAPTKCK RRVVQ RRRR RR

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Macromolecule #2: AMC016 gp41

MacromoleculeName: AMC016 gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.311746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGTIGAMFL GFLGAAGSTM GAASMTLTVQ ARQLLSGIVQ QQSNLLRAPE AQQHLLKLTV WGIKQLQARV LAVERYLKDQ QLLGIWGCS GKLICCTAVP WNASWSNKSL DNIWNNMTWM EWEKEISNYT NLIYNLIEES QNQQEKNEQE LLELD

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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: 45 / 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
GridModel: C-flat-2/2
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: 3801 / Average exposure time: 7.0 sec. / Average electron dose: 40.0 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 77068
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-7rso:
AMC016 SOSIP.v4.2 in complex with PGV04 Fab

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