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- EMDB-22569: CryoEM polyclonal immune complex of Fab binding the stem of H5 HA... -

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Basic information

Entry
Database: EMDB / ID: EMD-22569
TitleCryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28
Map dataCryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28
Sample
  • Complex: CryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsWard A / Han J / Richey ST
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Cell Rep / Year: 2021
Title: Polyclonal epitope mapping reveals temporal dynamics and diversity of human antibody responses to H5N1 vaccination.
Authors: Julianna Han / Aaron J Schmitz / Sara T Richey / Ya-Nan Dai / Hannah L Turner / Bassem M Mohammed / Daved H Fremont / Ali H Ellebedy / Andrew B Ward /
Abstract: Novel influenza A virus (IAV) strains elicit recall immune responses to conserved epitopes, making them favorable antigenic choices for universal influenza virus vaccines. Evaluating these immunogens ...Novel influenza A virus (IAV) strains elicit recall immune responses to conserved epitopes, making them favorable antigenic choices for universal influenza virus vaccines. Evaluating these immunogens requires a thorough understanding of the antigenic sites targeted by the polyclonal antibody (pAb) response, which single-particle electron microscopy (EM) can sensitively detect. In this study, we employ EM polyclonal epitope mapping (EMPEM) to extensively characterize the pAb response to hemagglutinin (HA) after H5N1 immunization in humans. Cross-reactive pAbs originating from memory B cells immediately bound the stem of HA and persisted for more than a year after vaccination. In contrast, de novo pAb responses to multiple sites on the head of HA, targeting previously determined key neutralizing sites on H5 HA, expanded after the second immunization and waned quickly. Thus, EMPEM provides a robust tool for comprehensively tracking the specificity and durability of immune responses elicited by novel universal influenza vaccine candidates.
History
DepositionSep 2, 2020-
Header (metadata) releaseFeb 10, 2021-
Map releaseFeb 10, 2021-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0156
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0156
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22569.png

Downloads & links

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Map

FileDownload / File: emd_22569.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0156 / Movie #1: 0.0156
Minimum - Maximum-0.044490445 - 0.10579926
Average (Standard dev.)9.906467e-05 (±0.003100114)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.600329.600329.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0440.1060.000

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Supplemental data

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Mask #1

Fileemd_22569_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 for CryoEM polyclonal immune complex...

Fileemd_22569_half_map_1.map
AnnotationHalf map 1 for CryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for CryoEM polyclonal immune complex...

Fileemd_22569_half_map_2.map
AnnotationHalf map 2 for CryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM polyclonal immune complex of Fab binding the stem of H5 HA...

EntireName: CryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28
Components
  • Complex: CryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28

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Supramolecule #1: CryoEM polyclonal immune complex of Fab binding the stem of H5 HA...

SupramoleculeName: CryoEM polyclonal immune complex of Fab binding the stem of H5 HA from serum of subject 4 at day 28
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Location in cell: PBMC

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 53.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 3.0)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4k62

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 25106
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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