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- EMDB-49185: Negative stain EM map of H1 HA (A/California/4/2009) in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-49185
TitleNegative stain EM map of H1 HA (A/California/4/2009) in complex with monoclonal fab ST4
Map dataNegative stain EM map of H1 HA (A/California/4/2009) in complex with monoclonal fab ST4
Sample
  • Complex: H1 HA (A/California/4/2009) in complex with monoclonal Fab ST4
    • Complex: H1 HA (A/California/4/2009)
    • Complex: ST4 monoclonal Fab
Keywordsinfluenza / hemagglutinin / H1 / 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
AuthorsRodriguez 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)75N39019C00051 United States
CitationJournal: To Be Published
Title: Individualized IG genotyping coupled with high throughput isolation of influenza HA-specific monoclonal antibodies
Authors: Fisher A / Corcoran M / Chernyshev M / Brouwer PJM / Gillespie R / Nicoletto A / Loeffler JR / Ferguson JA / Rodriguez AJ / Narang S / Adori M / Angeletti D / van Gils MJ / Castro Dopico X / ...Authors: Fisher A / Corcoran M / Chernyshev M / Brouwer PJM / Gillespie R / Nicoletto A / Loeffler JR / Ferguson JA / Rodriguez AJ / Narang S / Adori M / Angeletti D / van Gils MJ / Castro Dopico X / Kanekiyo M / Ward AB / Han J / Karlsson Hedestam GB
History
DepositionFeb 11, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49185.png

Downloads & links

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Map

FileDownload / File: emd_49185.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of H1 HA (A/California/4/2009) in complex with monoclonal fab ST4
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: 0.0161
Minimum - Maximum-0.021149999 - 0.08040393
Average (Standard dev.)0.00035425363 (±0.0041977107)
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 A of H1...

Fileemd_49185_half_map_1.map
AnnotationNegative stain EM half map A of H1 HA (A/California/4/2009) in complex with monoclonal fab ST4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain EM half map B of H1...

Fileemd_49185_half_map_2.map
AnnotationNegative stain EM half map B of H1 HA (A/California/4/2009) in complex with monoclonal fab ST4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H1 HA (A/California/4/2009) in complex with monoclonal Fab ST4

EntireName: H1 HA (A/California/4/2009) in complex with monoclonal Fab ST4
Components
  • Complex: H1 HA (A/California/4/2009) in complex with monoclonal Fab ST4
    • Complex: H1 HA (A/California/4/2009)
    • Complex: ST4 monoclonal Fab

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Supramolecule #1: H1 HA (A/California/4/2009) in complex with monoclonal Fab ST4

SupramoleculeName: H1 HA (A/California/4/2009) in complex with monoclonal Fab ST4
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: H1 HA (A/California/4/2009)

SupramoleculeName: H1 HA (A/California/4/2009) / type: complex / ID: 2 / Parent: 1 / Details: E47K stabilizing mutation in HA2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: ST4 monoclonal Fab

SupramoleculeName: ST4 monoclonal Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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

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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: 0.5 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:

4m4y

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: 1106
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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