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- EMDB-43689: nsEM map of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09 -

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Basic information

Entry
Database: EMDB / ID: EMD-43689
TitlensEM map of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09
Map datansEM map of NHP RKr9wk34 polyclonal Fab in complex with H1 Cali09
Sample
  • Complex: nsEM map of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09
    • Complex: Polyclonal Fab from NHP RKr19wk34
KeywordsEMPEM / polyclonal / HA / H1 / Cali09 / stem / antibody / Fab / vaccination / NHP / VIRAL PROTEIN
Biological speciesInfluenza A virus / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / negative staining / Resolution: 27.0 Å
AuthorsTurner HL / Ferguson JA / 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: nsEM map of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09
Authors: Styles TM / Akhtar A / Gu C / Neumann G / Muramatsu H / McPartlan J / Gratz D / Tharp G / Turner HL / Ferguson JA / Rodriguez AJ / Loganathan M / Manuel Carreno J / Francis B / Qin Z / Han J ...Authors: Styles TM / Akhtar A / Gu C / Neumann G / Muramatsu H / McPartlan J / Gratz D / Tharp G / Turner HL / Ferguson JA / Rodriguez AJ / Loganathan M / Manuel Carreno J / Francis B / Qin Z / Han J / Ward AB / Chahal J / Pardi N / Kawaoka Y / Krammer F / Ahmed R / Amara RR
History
DepositionFeb 12, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43689.png

Downloads & links

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Map

FileDownload / File: emd_43689.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationnsEM map of NHP RKr9wk34 polyclonal Fab in complex with H1 Cali09
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 160 pix.
= 266.72 Å		1.67 Å/pix.
x 160 pix.
= 266.72 Å		1.67 Å/pix.
x 160 pix.
= 266.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0121
Minimum - Maximum-0.025186418 - 0.09060754
Average (Standard dev.)0.00013263227 (±0.0044156983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 266.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09

Fileemd_43689_half_map_1.map
AnnotationHalf map 1 of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09

Fileemd_43689_half_map_2.map
AnnotationHalf map 2 of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : nsEM map of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09

EntireName: nsEM map of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09
Components
  • Complex: nsEM map of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09
    • Complex: Polyclonal Fab from NHP RKr19wk34

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Supramolecule #1: nsEM map of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09

SupramoleculeName: nsEM map of NHP RKr19wk34 polyclonal Fab in complex with H1 Cali09
type: complex / ID: 1 / Parent: 0 / Details: HA has E47K stabilizing mutation in HA2
Source (natural)Organism: Influenza A virus / Strain: A/California/07/2009

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Supramolecule #2: Polyclonal Fab from NHP RKr19wk34

SupramoleculeName: Polyclonal Fab from NHP RKr19wk34 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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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

BufferpH: 7.4 / Details: TBS
StainingType: NEGATIVE / Material: Uranyl Formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS

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Electron microscopy

MicroscopeFEI TECNAI F20
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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3lzg

Final reconstructionResolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 7034
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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