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- EMDB-48695: Negative stain map of A/Red-tailed hawk/New York/NYCVH 22-8477/20... -

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Basic information

Entry
Database: EMDB / ID: EMD-48695
TitleNegative stain map of A/Red-tailed hawk/New York/NYCVH 22-8477/2022 H5 in complex with monoclonal Fab 6G1
Map dataNegative stain map of H5 HA (A/Red-tailed hawk/New York/NYCVH 22-8477/2022) in complex with monoclonal Fab 6G1
Sample
  • Complex: Negative stain EM map of H5 HA (A/Red-tailed hawk/New York/NYCVH 22-8477/2022) in complex with monoclonal Fab 6G1
Keywordsinfluenza / hemagglutinin / H5 / monoclonal / complex / fab complex / viral fusion protein / VIRAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 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_48695.png

Downloads & links

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Map

FileDownload / File: emd_48695.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain map of H5 HA (A/Red-tailed hawk/New York/NYCVH 22-8477/2022) in complex with monoclonal Fab 6G1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 216 pix.
= 427.68 Å		1.98 Å/pix.
x 216 pix.
= 427.68 Å		1.98 Å/pix.
x 216 pix.
= 427.68 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: 0.0211
Minimum - Maximum-0.06245554 - 0.105095744
Average (Standard dev.)0.000039268787 (±0.004043243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 427.68 Å
α=β=γ: 90.0 °

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Supplemental data

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

Fileemd_48695_half_map_1.map
AnnotationNegative stain half map B of H5 HA (A/Red-tailed Hawk/New York/NYCVH 22-8477/2022) in complex with monoclonal fab 6G1
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 H5 HA...

Fileemd_48695_half_map_2.map
AnnotationNegative stain half map A of H5 HA (A/Red-tailed Hawk/New York/NYCVH 22-8477/2022) in complex with monoclonal fab 6G1
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/Red-tailed hawk/New York/NYCVH ...

EntireName: Negative stain EM map of H5 HA (A/Red-tailed hawk/New York/NYCVH 22-8477/2022) in complex with monoclonal Fab 6G1
Components
  • Complex: Negative stain EM map of H5 HA (A/Red-tailed hawk/New York/NYCVH 22-8477/2022) in complex with monoclonal Fab 6G1

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Supramolecule #1: Negative stain EM map of H5 HA (A/Red-tailed hawk/New York/NYCVH ...

SupramoleculeName: Negative stain EM map of H5 HA (A/Red-tailed hawk/New York/NYCVH 22-8477/2022) in complex with monoclonal Fab 6G1
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
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 TALOS ARCTICA
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 opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal magnification: 73000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

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

4k62

Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 7100
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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