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- EMDB-23152: Cryo-electron microscopy reconstruction of antibody DH898.1 Fab-d... -

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Entry
Database: EMDB / ID: EMD-23152
TitleCryo-electron microscopy reconstruction of antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848 10.17 SOSIP trimer
Map dataFinal sharpened, locally filtered, map of antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848 10.17 SOSIP trimer
Sample
  • Complex: Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
    • Complex: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
      • Protein or peptide: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664
    • Complex: Antibody DH898.1 Fragment antigen binding (Fab) dimer
      • Protein or peptide: DH898.1 Fab heavy chain
      • Protein or peptide: DH898.1 Fab light chain
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsEdwards RJ / Acharya P
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI140897 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145687 United States
Citation
Journal: Cell / Year: 2021
Title: Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.
Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler ...Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler Evangelous / Bhavna Hora / Madison Berry / A Yousef Abuahmad / Jordan Sprenz / Margaret Deyton / Victoria Stalls / Megan Kopp / Allen L Hsu / Mario J Borgnia / Guillaume B E Stewart-Jones / Matthew S Lee / Naomi Bronkema / M Anthony Moody / Kevin Wiehe / Todd Bradley / S Munir Alam / Robert J Parks / Andrew Foulger / Thomas Oguin / Gregory D Sempowski / Mattia Bonsignori / Celia C LaBranche / David C Montefiori / Michael Seaman / Sampa Santra / John Perfect / Joseph R Francica / Geoffrey M Lynn / Baptiste Aussedat / William E Walkowicz / Richard Laga / Garnett Kelsoe / Kevin O Saunders / Daniela Fera / Peter D Kwong / Robert A Seder / Alberto Bartesaghi / George M Shaw / Priyamvada Acharya / Barton F Haynes /
Abstract: Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) ...Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (V) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without V-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgMIgDCD27, thus suggesting that they originated from a pool of antigen-experienced IgM or marginal zone B cells.
#1: Journal: bioRxiv / Year: 2020
Title: Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques
Authors: Williams WB / Meyerhoff RR / Edwards RJ / Li H / Nicely NI / Henderson R / Zhou Y / Janowska K / Mansouri K / Manne K / Stalls V / Hsu AL / Borgnia MJ / Stewart-Jones G / Lee MS / Bronkema N ...Authors: Williams WB / Meyerhoff RR / Edwards RJ / Li H / Nicely NI / Henderson R / Zhou Y / Janowska K / Mansouri K / Manne K / Stalls V / Hsu AL / Borgnia MJ / Stewart-Jones G / Lee MS / Bronkema N / Perfect J / Moody MA / Wiehe K / Bradley T / Kepler TB / Alam SM / Foulger A / Bonsignori M / LaBranche CC / Montefiori DC / Seaman M / Santra S / Francica JR / Lynn GM / Aussedat B / Walkowicz WE / Laga R / Kelso G / Saunders KO / Fera D / Kwong PD / Seder RA / Bartesaghi A / Shaw GM / Acharya P / Haynes BF
History
DepositionDec 17, 2020-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateJun 9, 2021-
Current statusJun 9, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.65
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.65
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23152.png

Downloads & links

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Map

FileDownload / File: emd_23152.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal sharpened, locally filtered, map of antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848 10.17 SOSIP trimer
Voxel sizeX=Y=Z: 1.0665 Å
Density
Contour LevelBy AUTHOR: 0.65 / Movie #1: 0.65
Minimum - Maximum-1.0151678 - 2.4332495
Average (Standard dev.)0.015631182 (±0.099575594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 341.27872 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0664968751.0664968751.066496875
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z341.279341.279341.279
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.0152.4330.016

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Supplemental data

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Mask #1

Fileemd_23152_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_23152_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unmodified final map of antibody DH898.1 Fab-dimer bound...

Fileemd_23152_additional_1.map
AnnotationUnmodified final map of antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848 10.17 SOSIP trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local resolution of final map of antibody DH898.1...

Fileemd_23152_additional_2.map
AnnotationLocal resolution of final map of antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848 10.17 SOSIP trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A of antibody DH898.1 Fab-dimer bound to...

Fileemd_23152_half_map_1.map
AnnotationHalf-map A of antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848 10.17 SOSIP trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of antibody DH898.1 Fab-dimer bound to...

Fileemd_23152_half_map_2.map
AnnotationHalf-map B of antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848 10.17 SOSIP trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of ...

EntireName: Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
Components
  • Complex: Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
    • Complex: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
      • Protein or peptide: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664
    • Complex: Antibody DH898.1 Fragment antigen binding (Fab) dimer
      • Protein or peptide: DH898.1 Fab heavy chain
      • Protein or peptide: DH898.1 Fab light chain

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Supramolecule #1: Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of ...

SupramoleculeName: Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 94 KDa

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Supramolecule #2: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer

SupramoleculeName: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: CH848 10.17
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

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Supramolecule #3: Antibody DH898.1 Fragment antigen binding (Fab) dimer

SupramoleculeName: Antibody DH898.1 Fragment antigen binding (Fab) dimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: Composed of two heavy chains and two light chains
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

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Macromolecule #1: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664

MacromoleculeName: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: CH848.3.D0949.10.17
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPCV KLTPLCVTLI CSNATVKNGT VEEMKNCSFN TTTEIRDKEK KEYALFYKPD IVPLSETNNT SEYRLINCNT SACTQACPKV ...String:
AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPCV KLTPLCVTLI CSNATVKNGT VEEMKNCSFN TTTEIRDKEK KEYALFYKPD IVPLSETNNT SEYRLINCNT SACTQACPKV TFEPIPIHYC APAGYAILKC NDETFNGTGP CSNVSTVQCT HGIRPVVSTQ LLLNGSLAEK EIVIRSENLT NNAKIIIVHL HTPVEIVCTR PNNNTRKSVR IGPGQTFYAT GDIIGDIKQA HCNISEEKWN DTLQKVGIEL QKHFPNKTIK YNQSAGGDME ITTHSFNCGG EFFYCNTSNL FNGTYNGTYI STNSSANSTS TITLQCRIKQ IINMWQGVGR CMYAPPIAGN ITCRSNITGL LLTRDGGTNS NETETFRPAG GDMRDNWRSE LYKYKVVKIE PLGVAPTRCK RRVVGRRRRR RAVGIGAVFL GFLGAAGSTM GAASMTLTVQ ARNLLSGIVQ QQSNLLRAPE AQQHLLKLTV WGIKQLQARV LAVERYLRDQ QLLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #2: DH898.1 Fab heavy chain

MacromoleculeName: DH898.1 Fab heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QDLLLQSGAE VREPGASVTV SCQASNYTFP DYYIHWVRLV PGQGLEWLGE MKPKVGVTNV SKKIRDRLFM TADTSTDTAY MVLSALTPGD TAIYYCTRLE PDFLSGWAHW GKGVLVTVSP ASTKGPSVFP LAPSSRSTSE STAALGCLVK DYFPEPVTVS WNSGSLTSGV ...String:
QDLLLQSGAE VREPGASVTV SCQASNYTFP DYYIHWVRLV PGQGLEWLGE MKPKVGVTNV SKKIRDRLFM TADTSTDTAY MVLSALTPGD TAIYYCTRLE PDFLSGWAHW GKGVLVTVSP ASTKGPSVFP LAPSSRSTSE STAALGCLVK DYFPEPVTVS WNSGSLTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YVCNVNHKPS NTKVDKRVE

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Macromolecule #3: DH898.1 Fab light chain

MacromoleculeName: DH898.1 Fab light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVMTQTPLS LSVTPGEPAS LSCRSSASLL HGNGNTYLHW YLRKAGQSPQ LLIFGGSKRV PGISDRFIGS GAGTNFTLKI SSVEADDVGF YYCAQGVAFP WTFGQGTKVE IKRAVAAPSV FIFPPSEDQV KSGTVSVVCL LNNFYPREAS VKWKVDGVLK TGNSQESVTE ...String:
EIVMTQTPLS LSVTPGEPAS LSCRSSASLL HGNGNTYLHW YLRKAGQSPQ LLIFGGSKRV PGISDRFIGS GAGTNFTLKI SSVEADDVGF YYCAQGVAFP WTFGQGTKVE IKRAVAAPSV FIFPPSEDQV KSGTVSVVCL LNNFYPREAS VKWKVDGVLK TGNSQESVTE QDSKDNTYSL SSTLTLSNTD YQSHNVYACE VTHQGLSSPV TKSFNRGE

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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

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
5.0 mMHEPES buffer
150.0 mMsodium chlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 12.0 nm
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP
Details: 2.5 microliters of sample applied to grid and incubated for 30 seconds in chamber, blotted for 2.5 seconds, and plunge frozen in liquid ethane.
DetailsFor the DH898.1-bound complex, purified HIV-1 Env was mixed with 6-fold molar excess of recombinantly expressed and purified DH898.1 Fab to obtain a final Env concentration of 1.5 mg/ml, and incubated for 2 hours at room temperature.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3230 / Average exposure time: 4.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1655400
Details: Particles were picked using Blob Picker on 500 micrographs with a minimum and maximum particle diameter of 150 and 250 angstroms for circular blobs, yielding 259,587 particles, which were ...Details: Particles were picked using Blob Picker on 500 micrographs with a minimum and maximum particle diameter of 150 and 250 angstroms for circular blobs, yielding 259,587 particles, which were extracted with a 320-pixel box size and subjected to 2D class averaging with 100 classes. From these, seven classes were chosen for template picking applied to the full final micrograph set, yielding 1,655,400 particles
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.10)
Startup modelType of model: INSILICO MODEL / In silico model: ab initio generated directly from data.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 14873
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 10132 / Software - Name: cryoSPARC (ver. 2.15.0) / Details: Ab initio
FSC plot (resolution estimation)

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