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- EMDB-49964: Global map of six VRC35 Fabs and three MEDI8852 Fabs bound to inf... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49964
TitleGlobal map of six VRC35 Fabs and three MEDI8852 Fabs bound to influenza H3N2 Victoria 2011 hemaglutinin
Map data
Sample
  • Complex: Cryo-EM structure of influenza H3N2 Victoria 2011 hemagglutinin bound with VRC35 Fab and MEDI8852 Fab
Keywordsbroadly neutralizing antibody / cryo-EM / hemagglutinin / high mannose / homotypic interactions / influenza A virus / multimeric recognition / N-linked glycan / ANTIVIRAL PROTEIN / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsCheng J / Cale EM / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS ...Cheng J / Cale EM / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS / Becker JE / Tsybovsky Y / Li N / Zhang B / Du H / Rubin S / Shapiro L / Pierson TC / Doria-Rose NA / Kwong PD / Zhou T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Global map of six VRC35 Fabs and three MEDI8852 Fabs bound to influenza H3N2 Victoria 2011 hemaglutinin
Authors: Cheng J / Cale EM / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS / Becker JE / Tsybovsky Y / Li N / Zhang B / Du H / Rubin S / Shapiro L / Pierson TC / ...Authors: Cheng J / Cale EM / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS / Becker JE / Tsybovsky Y / Li N / Zhang B / Du H / Rubin S / Shapiro L / Pierson TC / Doria-Rose NA / Kwong PD / Zhou T
History
DepositionApr 1, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49964.png

Downloads & links

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Map

FileDownload / File: emd_49964.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.048
Minimum - Maximum-0.08804113 - 0.25782666
Average (Standard dev.)0.00022583731 (±0.009859529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 348.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49964_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_49964_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 : Cryo-EM structure of influenza H3N2 Victoria 2011 hemagglutinin b...

EntireName: Cryo-EM structure of influenza H3N2 Victoria 2011 hemagglutinin bound with VRC35 Fab and MEDI8852 Fab
Components
  • Complex: Cryo-EM structure of influenza H3N2 Victoria 2011 hemagglutinin bound with VRC35 Fab and MEDI8852 Fab

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Supramolecule #1: Cryo-EM structure of influenza H3N2 Victoria 2011 hemagglutinin b...

SupramoleculeName: Cryo-EM structure of influenza H3N2 Victoria 2011 hemagglutinin bound with VRC35 Fab and MEDI8852 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5jw4

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1780000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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