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- EMDB-25810: Human Metapneumovirus F trimer in complex with M4B06 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-25810
TitleHuman Metapneumovirus F trimer in complex with M4B06 Fab
Map data
Sample
  • Complex: hMPV F trimer in complex with M4B06 Fab
KeywordsNeutralizing antibody / metapneumovirus / fusion protein / ANTIVIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsXiao X / Tian D / Yan X / Eddins NJ / Galli JD / Su H / Vora KA / Chen Z / Zhang L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Profiling of hMPV F-specific antibodies isolated from human memory B cells.
Authors: Xiao Xiao / Arthur Fridman / Lu Zhang / Pavlo Pristatsky / Eberhard Durr / Michael Minnier / Aimin Tang / Kara S Cox / Zhiyun Wen / Renee Moore / Dongrui Tian / Jennifer D Galli / Scott ...Authors: Xiao Xiao / Arthur Fridman / Lu Zhang / Pavlo Pristatsky / Eberhard Durr / Michael Minnier / Aimin Tang / Kara S Cox / Zhiyun Wen / Renee Moore / Dongrui Tian / Jennifer D Galli / Scott Cosmi / Michael J Eddins / Nicole L Sullivan / Xiaodong Yan / Andrew J Bett / Hua-Poo Su / Kalpit A Vora / Zhifeng Chen / Lan Zhang /
Abstract: Human metapneumovirus (hMPV) belongs to the Pneumoviridae family and is closely related to respiratory syncytial virus (RSV). The surface fusion (F) glycoprotein mediates viral fusion and is the ...Human metapneumovirus (hMPV) belongs to the Pneumoviridae family and is closely related to respiratory syncytial virus (RSV). The surface fusion (F) glycoprotein mediates viral fusion and is the primary target of neutralizing antibodies against hMPV. Here we report 113 hMPV-F specific monoclonal antibodies (mAbs) isolated from memory B cells of human donors. We characterize the antibodies' germline usage, epitopes, neutralization potencies, and binding specificities. We find that unlike RSV-F specific mAbs, antibody responses to hMPV F are less dominant against the apex of the antigen, and the majority of the potent neutralizing mAbs recognize epitopes on the side of hMPV F. Furthermore, neutralizing epitopes that differ from previously defined antigenic sites on RSV F are identified, and multiple binding modes of site V and II mAbs are discovered. Interestingly, mAbs that bind preferentially to the unprocessed prefusion F show poor neutralization potency. These results elucidate the immune recognition of hMPV infection and provide novel insights for future hMPV antibody and vaccine development.
History
DepositionDec 23, 2021-
Header (metadata) releaseMay 11, 2022-
Map releaseMay 11, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25810.png

Downloads & links

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Map

FileDownload / File: emd_25810.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.036091466 - 0.07941836
Average (Standard dev.)0.00013977998 (±0.0017586809)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25810_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_25810_half_map_1.map
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Half map: #1

Fileemd_25810_half_map_2.map
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Sample components

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Entire : hMPV F trimer in complex with M4B06 Fab

EntireName: hMPV F trimer in complex with M4B06 Fab
Components
  • Complex: hMPV F trimer in complex with M4B06 Fab

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Supramolecule #1: hMPV F trimer in complex with M4B06 Fab

SupramoleculeName: hMPV F trimer in complex with M4B06 Fab / type: complex / ID: 1 / Parent: 0
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: 7.5 / Details: 25 mM HEPES pH 7.5, 150 mM NaCl
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 75.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Initial model from dataset itself
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87876
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

5wb0


Chain - Source name: PDB / Chain - Initial model type: experimental model

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