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- EMDB-48688: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-48688
TitleNegative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 13E8
Map dataNegative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 13E8
Sample
  • Complex: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 13E8
Keywordsinfluenza / hemagglutinin / H5 / monoclonal / complex / fab complex / viral fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsLeon AN / Brouwer PJM / Rodriguez AJ / Han J / Ward AB
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: To Be Published
Title: Human Monoclonal Antibodies that Target Clade 2.3.4.4b H5N1 Hemagglutinin
Authors: Pena Alzua G / Leon AN / Brouwer PJM / Yellin T / Bhavsar D / Loganathan M / Bushfield K / Marizzi C / Rodriguez AJ / Han J / Webby R / Ward AB / Duty JA / Florian K
History
DepositionJan 16, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48688.png

Downloads & links

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Map

FileDownload / File: emd_48688.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 13E8
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 208 pix.
= 428.48 Å		2.06 Å/pix.
x 208 pix.
= 428.48 Å		2.06 Å/pix.
x 208 pix.
= 428.48 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: 0.0282
Minimum - Maximum-0.02065959 - 0.07236479
Average (Standard dev.)0.00015087526 (±0.0034767431)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 428.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Negative stain EM half map B of H5...

Fileemd_48688_half_map_1.map
AnnotationNegative stain EM half map B of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 13E8
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain EM half map A of H5...

Fileemd_48688_half_map_2.map
AnnotationNegative stain EM half map A of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 13E8
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex ...

EntireName: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 13E8
Components
  • Complex: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 13E8

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Supramolecule #1: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex ...

SupramoleculeName: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 13E8
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

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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 / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

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

6e7g

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: 1220
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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