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- EMDB-48822: Cryo-EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-48822
TitleCryo-EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fabs 1A1, 6G1, and CR9114.
Map data
Sample
  • Complex: H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 1A1, 6G1, and CR9114
Keywordsinfluenza / hemaglutinin / antibody-antigen complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 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 / Krammer F
History
DepositionJan 27, 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_48822.png

Downloads & links

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Map

FileDownload / File: emd_48822.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 500 pix.
= 362.5 Å		0.73 Å/pix.
x 500 pix.
= 362.5 Å		0.73 Å/pix.
x 500 pix.
= 362.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.15364903 - 0.22220556
Average (Standard dev.)0.000028828541 (±0.005778509)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 362.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48822_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48822_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48822_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 1A1, ...

EntireName: H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 1A1, 6G1, and CR9114
Components
  • Complex: H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 1A1, 6G1, and CR9114

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Supramolecule #1: H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 1A1, ...

SupramoleculeName: H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 1A1, 6G1, and CR9114
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 KDa

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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

Concentration0.527 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 42.39 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67555
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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