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- EMDB-49317: Polyclonal immune complex of Fab from serum of animal 2 at week 3... -

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Basic information

Entry
Database: EMDB / ID: EMD-49317
TitlePolyclonal immune complex of Fab from serum of animal 2 at week 35 binding H1 HA
Map dataNegative stain map of global refinement of particle stack used to sort polyclonal responses to H1 HA (A/California/04/2009 H1 (HA2 E47K)) from animal 2 week 35
Sample
  • Complex: Polyclonal immune complex of Fab from serum of animal 2 at week 35 binding H1 HA
    • Complex: Fab
    • Complex: hemagglutinin
Keywordsinfluenza virus / hemagglutinin / polyclonal antibody / VIRAL PROTEIN
Biological speciesMacaca mulatta (Rhesus monkey) / Influenza A virus
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 Å
AuthorsFerguson JA / Leon AN / Richey ST / Han J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Other government75N93019C00051 United States
CitationJournal: To Be Published
Title: AS03-adjuvanted chimeric HA-based influenza vaccine induces long-lived stalk-specific plasma cells in bone marrow and lymph nodes of non-human primates
Authors: Akhtar A / Styles TM / Gu C / Leon AN / Tharp GK / Stokdyk K / Abbad A / Hirst C / Strohmeier S / Neumann G / Richey ST / Ferguson JA / Ahmed H / Han J / Carreno JM / Davis CW / Antia R / ...Authors: Akhtar A / Styles TM / Gu C / Leon AN / Tharp GK / Stokdyk K / Abbad A / Hirst C / Strohmeier S / Neumann G / Richey ST / Ferguson JA / Ahmed H / Han J / Carreno JM / Davis CW / Antia R / Ward AB / Kawaoka Y / Krammer F / Ahmed R / Amara RR
History
DepositionFeb 19, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49317.png

Downloads & links

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Map

FileDownload / File: emd_49317.map.gz / Format: CCP4 / Size: 34.3 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 H1 HA (A/California/04/2009 H1 (HA2 E47K)) from animal 2 week 35
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 208 pix.
= 347.36 Å		1.67 Å/pix.
x 208 pix.
= 347.36 Å		1.67 Å/pix.
x 208 pix.
= 347.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0122
Minimum - Maximum-0.027042499 - 0.052781723
Average (Standard dev.)-0.000044130964 (±0.0026987721)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 347.36 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_49317_additional_1.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA central stem epitope from animal 2 week 35
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain half map B of global refinement...

Fileemd_49317_half_map_1.map
AnnotationNegative stain half map B of global refinement of particle stack used to sort polyclonal responses to H1 HA (A/California/04/2009 H1 (HA2 E47K)) from animal 2 week 35
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain half map A of global refinement...

Fileemd_49317_half_map_2.map
AnnotationNegative stain half map A of global refinement of particle stack used to sort polyclonal responses to H1 HA (A/California/04/2009 H1 (HA2 E47K)) from animal 2 week 35
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 from serum of animal 2 at week 3...

EntireName: Polyclonal immune complex of Fab from serum of animal 2 at week 35 binding H1 HA
Components
  • Complex: Polyclonal immune complex of Fab from serum of animal 2 at week 35 binding H1 HA
    • Complex: Fab
    • Complex: hemagglutinin

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Supramolecule #1: Polyclonal immune complex of Fab from serum of animal 2 at week 3...

SupramoleculeName: Polyclonal immune complex of Fab from serum of animal 2 at week 35 binding H1 HA
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 280 KDa

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Supramolecule #2: Fab

SupramoleculeName: Fab / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #3: hemagglutinin

SupramoleculeName: hemagglutinin / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Influenza A virus / Strain: A/California/04/2009 E47K

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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 20
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: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 73000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4m4y


Details: 30A map generated in Chimera and used as starting model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 1900
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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