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- EMDB-20882: B41 SOSIP.664 in complex with rabbit antibody 45A -

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Entry
Database: EMDB / ID: EMD-20882
TitleB41 SOSIP.664 in complex with rabbit antibody 45A
Map dataHIV-1 B41 SOSIP.664 in complex with rabbit antibody 45A map
Sample
  • Complex: HIV-1 B41 SOSIP.664 in complex with rabbit antibody 45A
    • Complex: HIV-1 B41 SOSIP.664
    • Complex: rabbit antibody 45A
Biological speciesHuman immunodeficiency virus 1 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / negative staining / Resolution: 18.0 Å
AuthorsYang YR / Ward AB / Cottrell CA / Turner HL
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUM1AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesP01 AI110657 United States
Bill & Melinda Gates FoundationOPP1115782 United States
CitationJournal: J Virol / Year: 2020
Title: Autologous Antibody Responses to an HIV Envelope Glycan Hole Are Not Easily Broadened in Rabbits.
Authors: Yuhe R Yang / Laura E McCoy / Marit J van Gils / Raiees Andrabi / Hannah L Turner / Meng Yuan / Christopher A Cottrell / Gabriel Ozorowski / James Voss / Matthias Pauthner / Thomas M ...Authors: Yuhe R Yang / Laura E McCoy / Marit J van Gils / Raiees Andrabi / Hannah L Turner / Meng Yuan / Christopher A Cottrell / Gabriel Ozorowski / James Voss / Matthias Pauthner / Thomas M Polveroni / Terrence Messmer / Ian A Wilson / Rogier W Sanders / Dennis R Burton / Andrew B Ward /
Abstract: Extensive studies with subtype A BG505-derived HIV envelope glycoprotein (Env) immunogens have revealed that the dominant autologous neutralizing epitope in rabbits is located in an exposed region of ...Extensive studies with subtype A BG505-derived HIV envelope glycoprotein (Env) immunogens have revealed that the dominant autologous neutralizing epitope in rabbits is located in an exposed region of the heavily glycosylated trimer that lacks potential N-linked glycosylation sites at positions 230, 241, and 289. The Env derived from B41, a subtype B virus, shares a glycan hole centered on positions 230 and 289. To test whether broader neutralization to the common glycan hole can be achieved, we immunized rabbits with B41 SOSIP (gp120-gp41 disulfide [SOS] with an isoleucine-to-proline mutation [IP] in gp41) alone, as well as B41 and BG505 coimmunization. We isolated autologous neutralizing antibodies (nAbs) and described their structure in complex with the B41 Env. Our data suggest that distinct autologous nAb lineages are induced by BG505 and B41 immunogens, even when both were administered together. In contrast to previously described BG505 glycan hole antibodies, the B41-specific nAbs accommodate the >97% conserved N241 glycan, which is present in B41. Single-particle cryo-electron microscopy studies confirmed that B41- and BG505-specific nAbs bind to overlapping glycan hole epitopes. We then used our high-resolution data to guide mutations in the BG505 glycan hole epitope in an attempt to broaden the reactivity of a B41-specific nAb, but we recovered only partial binding. Our data demonstrate that the lack of cross-reactivity in glycan hole antibodies is due to amino acid differences within the epitope, and our attempts to rationally design cross-reactive trimers resulted in only limited success. Thus, even for the immunodominant glycan hole shared between BG505 and B41, the prospect of designing prime-boost immunogens remains difficult. A glycan hole is one of the most dominant autologous neutralizing epitopes targeted on BG505 and B41 SOSIP trimer-immunized rabbits. Our high-resolution cryo-electron microscopy (cryoEM) studies of B41 in complex with a B41-specific antibody complex elucidate the molecular basis of this strain-specific glycan hole response. We conclude that even for the immunodominant glycan hole shared between BG505 and B41, the prospect of designing prime-boost immunogens remains difficult.
History
DepositionOct 30, 2019-
Header (metadata) releaseDec 4, 2019-
Map releaseJan 29, 2020-
UpdateApr 1, 2020-
Current statusApr 1, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.53
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.53
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20882.png

Downloads & links

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Map

FileDownload / File: emd_20882.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 B41 SOSIP.664 in complex with rabbit antibody 45A map
Voxel sizeX=Y=Z: 2.05 Å
Density
Contour LevelBy AUTHOR: 0.53 / Movie #1: 0.53
Minimum - Maximum-0.6997046 - 3.1245775
Average (Standard dev.)-0.022402775 (±0.19911379)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.7003.125-0.022

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Supplemental data

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Sample components

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Entire : HIV-1 B41 SOSIP.664 in complex with rabbit antibody 45A

EntireName: HIV-1 B41 SOSIP.664 in complex with rabbit antibody 45A
Components
  • Complex: HIV-1 B41 SOSIP.664 in complex with rabbit antibody 45A
    • Complex: HIV-1 B41 SOSIP.664
    • Complex: rabbit antibody 45A

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Supramolecule #1: HIV-1 B41 SOSIP.664 in complex with rabbit antibody 45A

SupramoleculeName: HIV-1 B41 SOSIP.664 in complex with rabbit antibody 45A
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 570 KDa

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Supramolecule #2: HIV-1 B41 SOSIP.664

SupramoleculeName: HIV-1 B41 SOSIP.664 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: B41
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293F

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Supramolecule #3: rabbit antibody 45A

SupramoleculeName: rabbit antibody 45A / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293F

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMsodium chlorideNaClSodium chloride
StainingType: NEGATIVE / Material: 2% Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus min: 1.5 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 0.5 sec. / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 5400

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