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- EMDB-23369: Polyclonal Immune complex of Fab binding to BG505 SOSIP.v4.1 from... -

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Basic information

Entry
Database: EMDB / ID: EMD-23369
TitlePolyclonal Immune complex of Fab binding to BG505 SOSIP.v4.1 from serum of rabbit 2214 at wk 43
Map dataPolyclonal Immune complex of Fab binding to BG505 SOSIP.v4.1 from serum of rabbit 2214 at wk 43
Sample
  • Complex: Polyclonal Immune complex of Fab binding to BG505 SOSIP.v4.1 from serum of rabbit 2214 at wk 43
    • Complex: Polyclonal Fabs
    • Complex: BG505 SOSIP.v4.1
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 / 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
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Human immunodeficiency virus
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsPratap PP / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: Elife / Year: 2021
Title: High-resolution mapping of the neutralizing and binding specificities of polyclonal sera post-HIV Env trimer vaccination.
Authors: Adam S Dingens / Payal Pratap / Keara Malone / Sarah K Hilton / Thomas Ketas / Christopher A Cottrell / Julie Overbaugh / John P Moore / P J Klasse / Andrew B Ward / Jesse D Bloom /
Abstract: Mapping polyclonal serum responses is critical to rational vaccine design. However, most high-resolution mapping approaches involve isolating and characterizing individual antibodies, which ...Mapping polyclonal serum responses is critical to rational vaccine design. However, most high-resolution mapping approaches involve isolating and characterizing individual antibodies, which incompletely defines the polyclonal response. Here we use two complementary approaches to directly map the specificities of the neutralizing and binding antibodies of polyclonal anti-HIV-1 sera from rabbits immunized with BG505 Env SOSIP trimers. We used mutational antigenic profiling to determine how all mutations in Env affected viral neutralization and electron microscopy polyclonal epitope mapping (EMPEM) to directly visualize serum Fabs bound to Env trimers. The dominant neutralizing specificities were generally only a subset of the more diverse binding specificities. Additional differences between binding and neutralization reflected antigenicity differences between virus and soluble Env trimer. Furthermore, we refined residue-level epitope specificity directly from sera, revealing subtle differences across sera. Together, mutational antigenic profiling and EMPEM yield a holistic view of the binding and neutralizing specificity of polyclonal sera.
History
DepositionJan 26, 2021-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMar 10, 2021-
Current statusMar 10, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0189
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0189
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23369.png

Downloads & links

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Map

FileDownload / File: emd_23369.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPolyclonal Immune complex of Fab binding to BG505 SOSIP.v4.1 from serum of rabbit 2214 at wk 43
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 192 pix.
= 380.16 Å		1.98 Å/pix.
x 192 pix.
= 380.16 Å		1.98 Å/pix.
x 192 pix.
= 380.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0189 / Movie #1: 0.0189
Minimum - Maximum-0.05784035 - 0.11491346
Average (Standard dev.)0.00022725765 (±0.0070190527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 380.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.981.981.98
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z380.160380.160380.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ296296296
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0580.1150.000

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Supplemental data

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Sample components

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Entire : Polyclonal Immune complex of Fab binding to BG505 SOSIP.v4.1 from...

EntireName: Polyclonal Immune complex of Fab binding to BG505 SOSIP.v4.1 from serum of rabbit 2214 at wk 43
Components
  • Complex: Polyclonal Immune complex of Fab binding to BG505 SOSIP.v4.1 from serum of rabbit 2214 at wk 43
    • Complex: Polyclonal Fabs
    • Complex: BG505 SOSIP.v4.1

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Supramolecule #1: Polyclonal Immune complex of Fab binding to BG505 SOSIP.v4.1 from...

SupramoleculeName: Polyclonal Immune complex of Fab binding to BG505 SOSIP.v4.1 from serum of rabbit 2214 at wk 43
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Polyclonal Fabs

SupramoleculeName: Polyclonal Fabs / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Location in cell: PBMC

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Supramolecule #3: BG505 SOSIP.v4.1

SupramoleculeName: BG505 SOSIP.v4.1 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus
Recombinant expressionOrganism: Homo sapiens (human)

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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: 2% w/v uranyl formate

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Electron microscopy

MicroscopeTFS TALOS F200C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1439
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1439
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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