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- EMDB-41542: Polyclonal immune complex of Fab binding the H2 HA from serum of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41542
TitlePolyclonal immune complex of Fab binding the H2 HA from serum of subject 3-3 at week 4
Map dataNegative stain map of global refinement of particle stack used to sort polyclonal responses to H2 HA from human subject 3-3 at week 4
Sample
  • Complex: Polyclonal immune complex of Fab binding the H2 HA from serum of subject 3-3 at week 4
Keywordsinfluenza / hemagglutinin / H2 / polyclonal complex / Fab complex / viral fusion protein / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsYang YR / Han J / Richey ST / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: To Be Published
Title: Mapping HA epitopes targeted by polyclonal antibodies following H2N2 vaccination in humans
Authors: Yang YR / Han J / Perrett HR / Richey ST / Jackson AM / Rodriguez AJ / Gillespie RA / O'Connell S / Raab JE / Cominsky LY / Chopde A / Kanekiyo M / Houser KV / Chen GL / McDermott AB / Andrews SF / Ward AB
History
DepositionAug 8, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41542.png

Downloads & links

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Map

FileDownload / File: emd_41542.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain map of global refinement of particle stack used to sort polyclonal responses to H2 HA from human subject 3-3 at week 4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 160 pix.
= 329.6 Å		2.06 Å/pix.
x 160 pix.
= 329.6 Å		2.06 Å/pix.
x 160 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0214
Minimum - Maximum-0.037549086 - 0.11915722
Average (Standard dev.)-0.00007058204 (±0.0043569934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_41542_additional_1.map
AnnotationNegative stain map of polyclonal Fab binding the H2 HA central stem epitope from human subject 3-3 at week 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_41542_additional_2.map
AnnotationNegative stain map of polyclonal Fab binding the H2 HA RBS epitope from human subject 3-3 at week 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain map of half map A for...

Fileemd_41542_half_map_1.map
AnnotationNegative stain map of half map A for global refinement of particle stack used to sort polyclonal responses to H2 HA from human subject 3-3 at week 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain map of half map B for...

Fileemd_41542_half_map_2.map
AnnotationNegative stain map of half map B for global refinement of particle stack used to sort polyclonal responses to H2 HA from human subject 3-3 at week 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polyclonal immune complex of Fab binding the H2 HA from serum of ...

EntireName: Polyclonal immune complex of Fab binding the H2 HA from serum of subject 3-3 at week 4
Components
  • Complex: Polyclonal immune complex of Fab binding the H2 HA from serum of subject 3-3 at week 4

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Supramolecule #1: Polyclonal immune complex of Fab binding the H2 HA from serum of ...

SupramoleculeName: Polyclonal immune complex of Fab binding the H2 HA from serum of subject 3-3 at week 4
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 KDa

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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

Concentration0.015 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: 2% w/v uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3ku5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 27331
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

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