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- EMDB-21062: RM19A1 Fab in complex with BG505 SOSIPv5.2 -

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Basic information

Entry
Database: EMDB / ID: EMD-21062
TitleRM19A1 Fab in complex with BG505 SOSIPv5.2
Map dataRM19A1 Fab in complex with BG505 SOSIPv5.2
Sample
  • Complex: RM19N Fab in complex with BG505 SOSIPv5.2
Biological speciesMacaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 Å
AuthorsCottrell CA / Ozorowski G / Ward AB
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesF31 AI131873 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesP01 AI110657 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUM1 AI100663 United States
Bill & Melinda Gates FoundationOPP1115782 United States
National Institutes of Health/Office of the DirectorS10 OD021634 United States
Citation
Journal: PLoS Pathog / Year: 2020
Title: Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates.
Authors: Christopher A Cottrell / Jelle van Schooten / Charles A Bowman / Meng Yuan / David Oyen / Mia Shin / Robert Morpurgo / Patricia van der Woude / Mariëlle van Breemen / Jonathan L Torres / ...Authors: Christopher A Cottrell / Jelle van Schooten / Charles A Bowman / Meng Yuan / David Oyen / Mia Shin / Robert Morpurgo / Patricia van der Woude / Mariëlle van Breemen / Jonathan L Torres / Raj Patel / Justin Gross / Leigh M Sewall / Jeffrey Copps / Gabriel Ozorowski / Bartek Nogal / Devin Sok / Eva G Rakasz / Celia Labranche / Vladimir Vigdorovich / Scott Christley / Diane G Carnathan / D Noah Sather / David Montefiori / Guido Silvestri / Dennis R Burton / John P Moore / Ian A Wilson / Rogier W Sanders / Andrew B Ward / Marit J van Gils /
Abstract: The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown ...The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.
#1: Journal: Biorxiv / Year: 2020
Title: Mapping the immunogenic landscape of native HIV-1 envelope trimers in non-human primates
Authors: Cottrell CA / van Schooten J / Bowman CA / Yuan M / Oyen D / Shin M / Morpurgo R / van der Woude P / van Breemen M / Torres JL / Patel R / Gross J / Sewall LM / Copps J / Ozorowski G / Sok D ...Authors: Cottrell CA / van Schooten J / Bowman CA / Yuan M / Oyen D / Shin M / Morpurgo R / van der Woude P / van Breemen M / Torres JL / Patel R / Gross J / Sewall LM / Copps J / Ozorowski G / Sok D / Rakasz EG / Labranche C / Vigdorovich V / Christley S / Sather DN / Montefiori D / Moore JP / Burton DR / Wilson IA / Sanders RW / Ward AB / van Gils MJ
History
DepositionDec 4, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseAug 19, 2020-
UpdateSep 16, 2020-
Current statusSep 16, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21062.png

Downloads & links

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Map

FileDownload / File: emd_21062.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRM19A1 Fab in complex with BG505 SOSIPv5.2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 192 pix.
= 393.6 Å		2.05 Å/pix.
x 192 pix.
= 393.6 Å		2.05 Å/pix.
x 192 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.044628553 - 0.086522155
Average (Standard dev.)-0.0000013436 (±0.004555203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 393.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ310310310
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0450.087-0.000

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Supplemental data

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Sample components

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Entire : RM19N Fab in complex with BG505 SOSIPv5.2

EntireName: RM19N Fab in complex with BG505 SOSIPv5.2
Components
  • Complex: RM19N Fab in complex with BG505 SOSIPv5.2

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Supramolecule #1: RM19N Fab in complex with BG505 SOSIPv5.2

SupramoleculeName: RM19N Fab in complex with BG505 SOSIPv5.2 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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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

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate
GridSupport film - Material: CELLULOSE ACETATE / Details: unspecified

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 27312
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 6311
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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