- EMDB-4714: Negative staining of antibodies cooperative complex formed by hum... -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-4714
Title
Negative staining of antibodies cooperative complex formed by human IgG1 mAb7B10 and mAb2C1 bound to the N. meningitidis antigen factor H binding protein (fHbp)
Map data
Negative staining of coop
Sample
Complex: Quaternary complex formed by mAb7B10, mAb2C1 and two molecules of fHbp
Organelle or cellular component: N.meningitidis antigen factor H binding protein (fHbp)
Biological species
Homo sapiens (human) / Neisseria meningitidis serogroup B (bacteria)
Method
single particle reconstruction / negative staining / Resolution: 28.0 Å
Journal: 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
Deposition
Mar 18, 2019
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Header (metadata) release
Apr 3, 2019
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Map release
Jul 17, 2019
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Update
Jul 17, 2019
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Current status
Jul 17, 2019
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_4714.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Negative staining of coop
Voxel size
X=Y=Z: 3.3 Å
Density
Contour Level
By AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum
-0.12410519 - 0.24199128
Average (Standard dev.)
0.00020917485 (±0.013542563)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-54
-54
-54
Dimensions
60
60
60
Spacing
60
60
60
Cell
A=B=C: 198.0 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
3.3
3.3
3.3
M x/y/z
60
60
60
origin x/y/z
0.000
0.000
0.000
length x/y/z
198.000
198.000
198.000
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
-54
-54
-54
NC/NR/NS
60
60
60
D min/max/mean
-0.124
0.242
0.000
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Supplemental data
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Sample components
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Entire : Quaternary complex formed by mAb7B10, mAb2C1 and two molecules of fHbp
Entire
Name: Quaternary complex formed by mAb7B10, mAb2C1 and two molecules of fHbp
Components
Complex: Quaternary complex formed by mAb7B10, mAb2C1 and two molecules of fHbp
Organelle or cellular component: N.meningitidis antigen factor H binding protein (fHbp)
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Supramolecule #1: Quaternary complex formed by mAb7B10, mAb2C1 and two molecules of fHbp
Supramolecule
Name: Quaternary complex formed by mAb7B10, mAb2C1 and two molecules of fHbp type: complex / ID: 1 / Parent: 0 Details: Cooperative couple of human IgG1 mAbs bound to an antigen
Source (natural)
Organism: Homo sapiens (human)
Recombinant expression
Organism: Mammalia (mammals)
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Supramolecule #2: N.meningitidis antigen factor H binding protein (fHbp)
Supramolecule
Name: 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 expression
Organism: Escherichia coli BL21(DE3) (bacteria)
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Experimental details
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Structure determination
Method
negative staining
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Buffer
pH: 8
Staining
Type: NEGATIVE / Material: 1% Uranyl Acetate
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Electron microscopy
Microscope
FEI/PHILIPS CM200FEG
Image recording
Film or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Average electron dose: 30.0 e/Å2
Electron beam
Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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Image processing
Final reconstruction
Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10000
Initial angle assignment
Type: OTHER
Final angle assignment
Type: PROJECTION MATCHING
FSC plot (resolution estimation)
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