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- EMDB-22820: BG505 SOSIP.664 in complex with the V3-targeting rhesus macaque a... -

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Basic information

Entry
Database: EMDB / ID: EMD-22820
TitleBG505 SOSIP.664 in complex with the V3-targeting rhesus macaque antibody 1485 and human gp120-gp41 interface antibody 8ANC195
Map dataunsharpened main map
Sample
  • Complex: Ternary complex of HIV-1 Env glycoprotein, BG505. SOSIP.664, with broadly neutralizing antibodies 1485 and 8ANC195
    • Protein or peptide: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Ab 1485 Heavy Chain
    • Protein or peptide: 8ANC195 Fab Heavy Chain
    • Protein or peptide: 8ANC195 Fab Light Chain
    • Protein or peptide: Ab 1485 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / 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 speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsBarnes CO / Bjorkman PJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150464-13 United States
CitationJournal: Elife / Year: 2020
Title: A broadly neutralizing macaque monoclonal antibody against the HIV-1 V3-Glycan patch.
Authors: Zijun Wang / Christopher O Barnes / Rajeev Gautam / Julio C Cetrulo Lorenzi / Christian T Mayer / Thiago Y Oliveira / Victor Ramos / Melissa Cipolla / Kristie M Gordon / Harry B Gristick / ...Authors: Zijun Wang / Christopher O Barnes / Rajeev Gautam / Julio C Cetrulo Lorenzi / Christian T Mayer / Thiago Y Oliveira / Victor Ramos / Melissa Cipolla / Kristie M Gordon / Harry B Gristick / Anthony P West / Yoshiaki Nishimura / Henna Raina / Michael S Seaman / Anna Gazumyan / Malcolm Martin / Pamela J Bjorkman / Michel C Nussenzweig / Amelia Escolano /
Abstract: A small fraction of HIV-1- infected humans develop broadly neutralizing antibodies (bNAbs) against HIV-1 that protect macaques from simian immunodeficiency HIV chimeric virus (SHIV). Similarly, a ...A small fraction of HIV-1- infected humans develop broadly neutralizing antibodies (bNAbs) against HIV-1 that protect macaques from simian immunodeficiency HIV chimeric virus (SHIV). Similarly, a small number of macaques infected with SHIVs develop broadly neutralizing serologic activity, but less is known about the nature of simian antibodies. Here, we report on a monoclonal antibody, Ab1485, isolated from a macaque infected with SHIVAD8 that developed broadly neutralizing serologic activity targeting the V3-glycan region of HIV-1 Env. Ab1485 neutralizes 38.1% of HIV-1 isolates in a 42-pseudovirus panel with a geometric mean IC50 of 0.055 µg/mLl and SHIVAD8 with an IC50 of 0.028 µg/mLl. Ab1485 binds the V3-glycan epitope in a glycan-dependent manner. A 3.5 Å cryo-electron microscopy structure of Ab1485 in complex with a native-like SOSIP Env trimer showed conserved contacts with the N332gp120 glycan and gp120 GDIR peptide motif, but in a distinct Env-binding orientation relative to human V3/N332gp120 glycan-targeting bNAbs. Intravenous infusion of Ab1485 protected macaques from a high dose challenge with SHIVAD8. We conclude that macaques can develop bNAbs against the V3-glycan patch that resemble human V3-glycan bNAbs.
History
DepositionOct 8, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateNov 4, 2020-
Current statusNov 4, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kde
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22820.png

Downloads & links

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Map

FileDownload / File: emd_22820.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened main map
Voxel sizeX=Y=Z: 0.897 Å
Density
Contour LevelBy AUTHOR: 0.011 / Movie #1: 0.01
Minimum - Maximum-0.056814946 - 0.097062685
Average (Standard dev.)-0.00003965507 (±0.0032045948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 279.864 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8970.8970.897
M x/y/z312312312
origin x/y/z0.0000.0000.000
length x/y/z279.864279.864279.864
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS312312312
D min/max/mean-0.0570.097-0.000

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Supplemental data

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Mask #1

Fileemd_22820_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional map

Fileemd_22820_additional_1.map
AnnotationAdditional map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of HIV-1 Env glycoprotein, BG505. SOSIP.664, with...

EntireName: Ternary complex of HIV-1 Env glycoprotein, BG505. SOSIP.664, with broadly neutralizing antibodies 1485 and 8ANC195
Components
  • Complex: Ternary complex of HIV-1 Env glycoprotein, BG505. SOSIP.664, with broadly neutralizing antibodies 1485 and 8ANC195
    • Protein or peptide: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Ab 1485 Heavy Chain
    • Protein or peptide: 8ANC195 Fab Heavy Chain
    • Protein or peptide: 8ANC195 Fab Light Chain
    • Protein or peptide: Ab 1485 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of HIV-1 Env glycoprotein, BG505. SOSIP.664, with...

SupramoleculeName: Ternary complex of HIV-1 Env glycoprotein, BG505. SOSIP.664, with broadly neutralizing antibodies 1485 and 8ANC195
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightExperimental: 600 KDa

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Macromolecule #1: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41

MacromoleculeName: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #2: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.864086 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVK LTPLCVTLQC TNVTNNITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ...String:
NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVK LTPLCVTLQC TNVTNNITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SVSTVQCTHG IKPVVSTQLL LNGSLAEEEV MI RSENITN NAKNILVQFN TPVQINCTRP NNNTRKSIRI GPGQAFYATG DIIGDIRQAH CNVSKATWNE TLGKVVKQLR KHF GNNTII RFANSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAM YAPPI QGVIRCVSNI TGLILTRDGG STNSTTETFR PGGGDMRDNW RSELYKYKVV KIEPLGVAPT RCKRRVVGRR RRRR

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Macromolecule #3: Ab 1485 Heavy Chain

MacromoleculeName: Ab 1485 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.236078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGPG LVKASETLSL TCTVSGYNIR SNNWWSWVRQ PPGKGLEWIG GVYANSEITN YNSSLKSRVS ISQDAWRNKF SLKLKSVTD ADTAVYYCVR GPNHWEYFDS GNNEYFEFWG QGALVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
EVQLVESGPG LVKASETLSL TCTVSGYNIR SNNWWSWVRQ PPGKGLEWIG GVYANSEITN YNSSLKSRVS ISQDAWRNKF SLKLKSVTD ADTAVYYCVR GPNHWEYFDS GNNEYFEFWG QGALVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSCDK

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Macromolecule #4: 8ANC195 Fab Heavy Chain

MacromoleculeName: 8ANC195 Fab Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.153283 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIHLVQSGTE VKKPGSSVTV SCKAYGVNTF GLYAVNWVRQ APGQSLEYIG QIWRWKSSAS HHFRGRVLIS AVDLTGSSPP ISSLEIKNL TSDDTAVYFC TTTSTYDRWS GLHHDGVMAF SSWGQGTLIS VSAASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QIHLVQSGTE VKKPGSSVTV SCKAYGVNTF GLYAVNWVRQ APGQSLEYIG QIWRWKSSAS HHFRGRVLIS AVDLTGSSPP ISSLEIKNL TSDDTAVYFC TTTSTYDRWS GLHHDGVMAF SSWGQGTLIS VSAASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSCDKT HH HHHH

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Macromolecule #5: 8ANC195 Fab Light Chain

MacromoleculeName: 8ANC195 Fab Light Chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.460047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPST LSASTGDTVR ISCRASQSIT GNWVAWYQQR PGKAPRLLIY RGAALLGGVP SRFRGSAAGT DFTLTIGNLQ AEDFGTFYC QQYDTYPGTF GQGTKVEVKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPST LSASTGDTVR ISCRASQSIT GNWVAWYQQR PGKAPRLLIY RGAALLGGVP SRFRGSAAGT DFTLTIGNLQ AEDFGTFYC QQYDTYPGTF GQGTKVEVKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #6: Ab 1485 Light Chain

MacromoleculeName: Ab 1485 Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.167529 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPPSV SGAPGQRVTI SCTGTSSNIE NYHAFWYQQF SGMAPKLLIR DNDKRPSGVS DRFSGSKSGA SASLTITGLQ TDDEADYYC QSYDSGLRSY IFASGTRLTV LGQPKASPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSALTQPPSV SGAPGQRVTI SCTGTSSNIE NYHAFWYQQF SGMAPKLLIR DNDKRPSGVS DRFSGSKSGA SASLTITGLQ TDDEADYYC QSYDSGLRSY IFASGTRLTV LGQPKASPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #17: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 17 / Number of copies: 34 / 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

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.02 MTris-HClTrisTris
0.12 MNaClSodium chloridesodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 0.15 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 3s blot, blot force 0.
Detailsmonodisperse

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1926 / Average exposure time: 3.6 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1074537
Startup modelType of model: OTHER / Details: ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 6 / Avg.num./class: 80000 / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 405519
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6udj

chain_id: G

6udj

chain_id: B
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 118 / Target criteria: Correlation coefficient
Output model

PDB-7kde:
BG505 SOSIP.664 in complex with the V3-targeting rhesus macaque antibody 1485 and human gp120-gp41 interface antibody 8ANC195

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