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- EMDB-11731: CryoEM structure of MIB in complex with a polyclonal goat Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-11731
TitleCryoEM structure of MIB in complex with a polyclonal goat Fab
Map data
SampleMycoplasma MIB protein in complex with a goat Fab
  • Putative immunoglobulin-blocking virulence protein
Function / homologyMycoplasma virulence, signal domain / Putative immunoglobulin-blocking virulence protein / IgG-blocking virulence domain / Putative immunoglobulin-blocking virulence protein
Function and homology information
Biological speciesMycoplasma mycoides subsp. capri str. GM12 (bacteria) / Mycoplasma mycoides subsp. capri (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsNottelet P / Bataille L / Gourgues G / Anger R / Lartigue C / Sirand-Pugnet P / Marza E / Fronzes R / Arfi Y
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Sci Adv / Year: 2021
Title: The mycoplasma surface proteins MIB and MIP promote the dissociation of the antibody-antigen interaction.
Authors: Pierre Nottelet / Laure Bataille / Geraldine Gourgues / Robin Anger / Carole Lartigue / Pascal Sirand-Pugnet / Esther Marza / Remi Fronzes / Yonathan Arfi /
Abstract: Mycoplasma immunoglobulin binding (MIB) and mycoplasma immunoglobulin protease (MIP) are surface proteins found in the majority of mycoplasma species, acting sequentially to capture antibodies and ...Mycoplasma immunoglobulin binding (MIB) and mycoplasma immunoglobulin protease (MIP) are surface proteins found in the majority of mycoplasma species, acting sequentially to capture antibodies and cleave off their V domains. Cryo-electron microscopy structures show how MIB and MIP bind to a Fab fragment in a "hug of death" mechanism. As a result, the orientation of the V and V domains is twisted out of alignment, disrupting the antigen binding site. We also show that MIB-MIP has the ability to promote the dissociation of the antibody-antigen complex. This system is functional in cells and protects mycoplasmas from antibody-mediated agglutination. These results highlight the key role of the MIB-MIP system in immunity evasion by mycoplasmas through an unprecedented mechanism, and open exciting perspectives to use these proteins as potential tools in the antibody field.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionSep 15, 2020-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateApr 7, 2021-
Current statusApr 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.84
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.84
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7adm
  • Surface level: 3.84
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7adm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11731.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.13 Å/pix.
x 160 pix.
= 180.8 Å
1.13 Å/pix.
x 160 pix.
= 180.8 Å
1.13 Å/pix.
x 160 pix.
= 180.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density
Contour LevelBy AUTHOR: 3.84 / Movie #1: 3.84
Minimum - Maximum-26.90279 - 31.343922
Average (Standard dev.)-2.7639252e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 180.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.131.131.13
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z180.800180.800180.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-26.90331.344-0.000

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Supplemental data

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Additional map: #1

Fileemd_11731_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_11731_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_11731_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Mycoplasma MIB protein in complex with a goat Fab

EntireName: Mycoplasma MIB protein in complex with a goat Fab / Number of components: 2

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Component #1: protein, Mycoplasma MIB protein in complex with a goat Fab

ProteinName: Mycoplasma MIB protein in complex with a goat Fab / Recombinant expression: No
SourceSpecies: Mycoplasma mycoides subsp. capri str. GM12 (bacteria)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria) / Strain: Rosetta

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Component #2: protein, Putative immunoglobulin-blocking virulence protein

ProteinName: Putative immunoglobulin-blocking virulence protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 84.962719 kDa
SourceSpecies: Mycoplasma mycoides subsp. capri (bacteria)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 0.77 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 3517059
3D reconstructionSoftware: cryoSPARC / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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