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- EMDB-7896: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3... -

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Basic information

Entry
Database: EMDB / ID: EMD-7896
TitleHIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
Map dataHIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
Sample
  • Complex: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Monoclonal antibody 10A light chain
    • Protein or peptide: Monoclonal antibody 10A heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / antigen binding / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / blood microparticle / viral protein processing ...immunoglobulin complex / immunoglobulin mediated immune response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / antigen binding / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / blood microparticle / 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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...: / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IgG heavy chain VDJ region / Ig kappa-b4 chain C region / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.71 Å
AuthorsTurner HL / Cottrell CA / Oyen D / Wilson IA / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
Bill & Melinda Gates FoundationOPP1115782 United States
CitationJournal: Immunity / Year: 2018
Title: Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization.
Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton ...Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton / Andrew B Ward / Lars Hangartner /
Abstract: Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a ...Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a barrier to fully understanding the humoral response to antigens and hinders rational vaccine design efforts. Here, we describe a method of characterizing polyclonal responses by using electron microscopy, and we applied this method to the immunization of rabbits with an HIV-1 envelope glycoprotein vaccine candidate, BG505 SOSIP.664. We detected known epitopes within the polyclonal sera and revealed how antibody responses evolved during the prime-boosting strategy to ultimately result in a neutralizing antibody response. We uncovered previously unidentified epitopes, including an epitope proximal to one recognized by human broadly neutralizing antibodies as well as potentially distracting non-neutralizing epitopes. Our method provides an efficient and semiquantitative map of epitopes that are targeted in a polyclonal antibody response and should be of widespread utility in vaccine and infection studies.
History
DepositionMay 23, 2018-
Header (metadata) releaseJul 4, 2018-
Map releaseSep 5, 2018-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6did
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7896.png

Downloads & links

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Map

FileDownload / File: emd_7896.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 300 pix.
= 345. Å		1.15 Å/pix.
x 300 pix.
= 345. Å		1.15 Å/pix.
x 300 pix.
= 345. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35 / Movie #1: 0.35
Minimum - Maximum-0.40159664 - 1.3945129
Average (Standard dev.)0.0036196986 (±0.060318965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 345.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z345.000345.000345.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.4021.3950.004

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Supplemental data

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Sample components

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Entire : HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3...

EntireName: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
Components
  • Complex: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Monoclonal antibody 10A light chain
    • Protein or peptide: Monoclonal antibody 10A heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3...

SupramoleculeName: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Model includes fitted atomic structures for HIV Env BG505 SOSIP (PDB ID: 5v8m) and 10A Fab (PDB ID: 6cjk).
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.064277 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ AMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R

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Macromolecule #2: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #3: Monoclonal antibody 10A light chain

MacromoleculeName: Monoclonal antibody 10A light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 23.047424 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQTPAS VEAAVGGTVA IKCQASQSIR SYLAWYQQKP GQPPKLLIYE ASKLASGVPS RFSGSGSGTQ FTLTISGVEC DDAATYYCQ RNYDSYSGAY YPNGFGGGTE VVVKGDPVAP SVLIFPPAAD QVATGTVTIV CVANKYFPDV TVTWEVDGTT Q TTGIENSK ...String:
DIVMTQTPAS VEAAVGGTVA IKCQASQSIR SYLAWYQQKP GQPPKLLIYE ASKLASGVPS RFSGSGSGTQ FTLTISGVEC DDAATYYCQ RNYDSYSGAY YPNGFGGGTE VVVKGDPVAP SVLIFPPAAD QVATGTVTIV CVANKYFPDV TVTWEVDGTT Q TTGIENSK TPQNSADCTY NLSSTLTLTS TQYNSHKEYT CKVTQGTTSV VQSFNRGDC

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Macromolecule #4: Monoclonal antibody 10A heavy chain

MacromoleculeName: Monoclonal antibody 10A heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 22.263018 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLVESGGGLV QPGASLTLTC TASGFSFSSD YYMCWVRQAP GKGLEWIACI WTANSISYYA RWAKGRFTIS KTSSTTVTLQ MTSLTAADT ATYFCARGGS GDGQSLWGPG TLVTVSSGQP KAPSVFPLAP CCGDTPSSTV TLGCLVKGYL PEPVTVTWNS G TLTNGVRT ...String:
QLVESGGGLV QPGASLTLTC TASGFSFSSD YYMCWVRQAP GKGLEWIACI WTANSISYYA RWAKGRFTIS KTSSTTVTLQ MTSLTAADT ATYFCARGGS GDGQSLWGPG TLVTVSSGQP KAPSVFPLAP CCGDTPSSTV TLGCLVKGYL PEPVTVTWNS G TLTNGVRT FPSVRQSSGL YSLSSVVSVT SSSQPVTCNV AHPATNTKVD KTVAPS

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 21 / 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

Concentration5.6 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Average exposure time: 8.5 sec. / Average electron dose: 52.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 170078
CTF correctionSoftware - Name: Gctf
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 161639
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6did:
HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1

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