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- EMDB-4713: Negative staining of antibodies cooperative complex formed by hum... -

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Entry
Database: EMDB / ID: EMD-4713
TitleNegative staining of antibodies cooperative complex formed by human fab7B10 and fab2C1 bound to the N. meningitidis antigen factor H binding protein (fHbp)
Map dataNegative staining of cooperative couple of human fab7B10 and fab2C1 bound to N.meningitidis antigen fHbp
Sample
  • Complex: Ternary complex formed by fAb7B10, fAb2C1 and a molecule of fHbp
    • Organelle or cellular component: N.meningitidis antigen factor H binding protein (fHbp)
Biological speciesHomo sapiens (human) / Neisseria meningitidis serogroup B (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 23.0 Å
AuthorsPeschiera I / Ferlenghi I / Melero R / Liljeroos LJ / Paccagnini E / Giusti F / Carazo JM / Sorzano COS / Scarselli M
CitationJournal: Commun Biol / Year: 2019
Title: Structural basis for cooperativity of human monoclonal antibodies to meningococcal factor H-binding protein.
Authors: Ilaria Peschiera / Maria Giuliani / Fabiola Giusti / Roberto Melero / Eugenio Paccagnini / Danilo Donnarumma / Werner Pansegrau / José M Carazo / Carlos O S Sorzano / Maria Scarselli / Vega ...Authors: Ilaria Peschiera / Maria Giuliani / Fabiola Giusti / Roberto Melero / Eugenio Paccagnini / Danilo Donnarumma / Werner Pansegrau / José M Carazo / Carlos O S Sorzano / Maria Scarselli / Vega Masignani / Lassi J Liljeroos / Ilaria Ferlenghi /
Abstract: Monoclonal antibody (mAb) cooperativity is a phenomenon triggered when mAbs couples promote increased bactericidal killing compared to individual partners. Cooperativity has been deeply investigated ...Monoclonal antibody (mAb) cooperativity is a phenomenon triggered when mAbs couples promote increased bactericidal killing compared to individual partners. Cooperativity has been deeply investigated among mAbs elicited by factor H-binding protein (fHbp), a surface-exposed lipoprotein and one of the key antigens included in both serogroup B meningococcus vaccine Bexsero and Trumenba. Here we report the structural and functional characterization of two cooperative mAbs pairs isolated from Bexsero vaccines. The 3D electron microscopy structures of the human mAb-fHbp-mAb cooperative complexes indicate that the angle formed between the antigen binding fragments (fAbs) assume regular angle and that fHbp is able to bind simultaneously and stably the cooperative mAbs pairs and human factor H (fH) in vitro. These findings shed light on molecular basis of the antibody-based mechanism of protection driven by simultaneous recognition of the different epitopes of the fHbp and underline that cooperativity is crucial in vaccine efficacy.
History
DepositionMar 18, 2019-
Header (metadata) releaseApr 3, 2019-
Map releaseJul 17, 2019-
UpdateJul 17, 2019-
Current statusJul 17, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4713.png

Downloads & links

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Map

FileDownload / File: emd_4713.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative staining of cooperative couple of human fab7B10 and fab2C1 bound to N.meningitidis antigen fHbp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.3 Å/pix.
x 60 pix.
= 198. Å		3.3 Å/pix.
x 60 pix.
= 198. Å		3.3 Å/pix.
x 60 pix.
= 198. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.1403328 - 0.29140595
Average (Standard dev.)-0.0002910064 (±0.01271074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-54-54-54
Dimensions606060
Spacing606060
CellA=B=C: 198.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.33.33.3
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z198.000198.000198.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-54-54-54
NC/NR/NS606060
D min/max/mean-0.1400.291-0.000

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Supplemental data

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Sample components

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Entire : Ternary complex formed by fAb7B10, fAb2C1 and a molecule of fHbp

EntireName: Ternary complex formed by fAb7B10, fAb2C1 and a molecule of fHbp
Components
  • Complex: Ternary complex formed by fAb7B10, fAb2C1 and a molecule of fHbp
    • Organelle or cellular component: N.meningitidis antigen factor H binding protein (fHbp)

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Supramolecule #1: Ternary complex formed by fAb7B10, fAb2C1 and a molecule of fHbp

SupramoleculeName: Ternary complex formed by fAb7B10, fAb2C1 and a molecule of fHbp
type: complex / ID: 1 / Parent: 0
Details: The cooperative couple of fab was generated using the same CDR region of the cooperative couple of human IgG1 mAb7B10 and mAb2C1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #2: N.meningitidis antigen factor H binding protein (fHbp)

SupramoleculeName: N.meningitidis antigen factor H binding protein (fHbp)
type: organelle_or_cellular_component / ID: 2 / Parent: 1
Details: Is a surface-exposed lipoprotein expressed at different levels among the strains and it is present as recombinant antigen in both vaccines against meningococcal serogroup B licensed so far
Source (natural)Organism: Neisseria meningitidis serogroup B (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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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: 8
StainingType: NEGATIVE / Material: 1% Uranyl acetate

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingFilm or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10000
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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